The limits of technology available to the USN, and questionable judgment by Halsey, came up against some crafty maneuvering and good luck based on improvisation by the IJN.

Simply put Halsey with the big fleet carriers was too far away for strikes or even additional recon to track Center Force later into the afternoon during daylight. The last daylight strikes on the task force which focused on Musashi ended around 3:30-4:00 in the afternoon. About the same time that Kuria ordered the main body of Center Force to turn around and at least fall back out of air range.

Any other daylight strikes launched by Halsey would have required landing after dark. This was done on occasion, notably at Philippine Sea, but was always a big risk. Not every pilot was trained up for night landings or navigation, and even for those who were it was a big risk, and drained the pilots. A bold choice when Halsey was still expecting to get word about sighting the remaining IJN carrier any time now and his forces in general were being blitzed by a series off attacks from ground based air, which would cost him the light carrier Princeton that afternoon.

That is not to say he had no night assets at hand, the USN had become rather effective at first using night fighters and strike aircraft with radar to protect the task force, but to start using it in an offensive role from the carriers or at least to scout. The light carrier Independence with Halsey carried a small air wing expressly dedicated to these missions and it did launch scouts both towards Kurita, and North towards the now spotted IJN carriers. But this was still an inexact process, and even until the end of the war there were always some chaff and false alarm scouting reports for commanders to have to sift through for actionable ones. But those search flights do turn up at least the possibility that Kurita had turned back around and might be coming through the San Bernardino straight towards the US landing beaches and where the second line fleets were concentrated.

So we have a threat that seemingly had decided they didn't want to tangle after getting a bloody nose in Kurita, and a new threat of unknown striking power in the carriers that Halsey could steam all night North and be in position for dawn strikes to knock them out early and decisively if all went to plan. So off he goes, fixating on what he saw as the real prize carriers hunting other carriers. He was also only then on the afternoon of the 24th back at full strength, he had previously sent off nearly half his carriers under John McCain Sr. to refit and refuel, but had to recall them when a battle was looming.

But yes that does open up a large gap in the US forces, though his was not the only force prepared to defend the US anchorage and rear line fleets. Kinkaid had massed his better combatant ships including escorts and his older battleships under Oldendorff to ambush the Southern Force in the shooting gallery of Surigao Straight. Theoretically if on the 25th of October Kurita had turned back those ships could at least get into position to screen the other US supporting units while Halsey got his birds in the air. He had also notified Nimitz of the plan that if he needed to he would detach his newer better fast battleships and some escorts under Willis Lee to cover his old position while he took his carriers North. But while Nimitz and Kinkaid may have assumed, and seem to have done so, Halsey meant this only as a possibility, and never made the decision to do so. Both to keep his direct escort against air attack at max strength, but also to up the chance no IJN carriers escaped by sinking them with gunfire if he had to.

That gap then is where Kurita slipped Center Force through in the San Bernardino straight where they could then turn South towards their targets and the US second line forces. Hence Nimitz's famous message to Halsey during the height of the action the morning of the 25th demanding that Halsey reply:

TURKEY TROTS TO WATER GG FROM CINCPAC ACTION COM THIRD FLEET INFO COMINCH CTF SEVENTY-SEVEN X WHERE IS RPT WHERE IS TASK FORCE THIRTY FOUR RR THE WORLD WONDERS.

So in the end smart seamanship by Kurita, though his and the other forces deathride was ordered so there was to be no retreat anyway(not that the USN was fully aware though) let him drop off USN radar literally for a time. While Halsey's fixation on finding the IJN carriers off Cape Engano and finishing them led him to ignore threats from all other sectors until that was dealt with and his poor communication(and in a sense poor coordination by Nimitz, and nobody on halsey's staff either wanted to contradict their boss or thought the rumblings of Kurita's advance accurate enough to be actionable) meant that Kinkaid and the rest of 7th Fleet had an in accurate understanding of who was guarding their Northern flank where. So at sunrise on the 25th Ziggy Sprauge and his escort carriers thought they had no reason to fear and would continue to support operations ashore and instead met Kurita and his big guns.

Yes its taken from Wiki but I rather think this map is very helpful in understanding the positioning of the the USN and IJN forces, notice especially the position of Halsey's carrier groups and his bringing them together to fight Ozawa's Northern Force, opening the door for Kurita. https://upload.wikimedia.org/wikipedia/commons/f/f8/Leyte_map_annotated.jpg

With hindsight, the USN did make many crucial errors in failing to provide a carrier group to protect the landings at Leyte, but at the time this wasn't really beyond current naval strategy. Ozawa's forces sailing to the north of Luzon provided a vital strategic target for Halsey, as even though his role allotted to him by Nimitz was to protect MacArthur's landings, both he and Kinkaid felt that the opportunity to destroy Japanese carrier forces was the Third Fleet's 'prime objective'. Combined with the principle of 'concentration of force', Halsey was compelled to sail northward with all four of his carrier task groups, leaving Leyte undefended.

Halsey was, however, well aware that Kurita's force was in the Sibuyan Sea with the clear motive of attacking the landings at Leyte. The force had lost four of its heavy cruisers off Palawan after an attack by USS Darter and Dace on the 23rd, with two sunk, and the day after had come under a massive US air attack which had sunk the Musashi. However, the Musashi was able to act as a decoy for the rest of Kurita's force, absorbing the full brunt of air attacks and allowing Kurita to withdraw most of his ships. It was assumed then by Halsey and most officers in the Third Fleet that Kurita had lost more ships than he actually had, and with the force already short on escorts and fuel oil, it seemed logical Kurita would be forced to return West. While Kurita's force was eventually picked up returning to the San Bernardino Strait, US reconaissance was patchy and poorly executed, and eventually called off as Ozawa's aircraft had attacked task force 38.3.

Miscommunication between Kinkaid and Halsey also played a role here, as Kinkaid had wired Halsey on the latter's decision to move three carrier task groups north against Ozawa, to which Halsey had failed to respond. Kinkaid had assumed that Halsey had left his fourth group in defence of San Bernardino. It was similarly assumed by most officers that a battleship group was being sent to San Bernardino, especially those onboard the USS New Jersey, who were then surprised the next morning to find the battleships accompanying the carriers on their way north. Kinkaid had also been, however, quick to allay Halsey that Kurita's force had been 'too heavily damaged' to be of any threat, and Halsey himself did not believe that Kurita could undertake a night action, or reach Leyte before nightfall.

Historiography hasn't been kind to Kurita, and it seems rightly so. His speech to his signals staff on 'miracles' and the 'self-sacrifical' role of Ozawa and Shimi's forces seem his only influence on the Battle off Samar being as close-knit as it was. The decision to return East came largely by command of Toyoda at Combined Fleet HQ, telling him to 'go with God' and 'charge'. His failure to provide adequate destroyer escort and the consequential loss of three cruisers, including his own flagship Atago, alongside the lack of air cover provided and the loss of Musashi inadvertantly caused the USN to believe Kurita's force too weak to be of any threat to the Leyte landings.

In sum, the the closeness battle off Samar resulted primarily from US tactical error. The failure of a battle-line being dispatched to San Bernardino, owing to miscommunication and Halsey's own eagerness to engage Ozawa led to Kurita being able to engage the landing force escorts. The battle at Surigao had also diverted Seventh Fleet attention toward Nishimura's force. Japanese tactics, as in Kurita's tactics, had little part to play. It was, for Kurita, pure luck that USN reconaissance aircraft did not pick up his force re-entering the Sibuyan Sea, the running aground of the Darter that prevented a re-engagement by submarines, and Halsey's paradoxical decision to leave Taffy 3 without escort.

Source:

H.P. Willmott. The Battle of Leyte Gulf: The Last Fleet Action. 2005.

Well the simple answer is poor staff work by Halsey and the 3rd Fleet allowed Kurita to surprise everyone by passing through the San Bernadino strait in darkness.

Kurita's force had been hit hard by submarines and aircraft from the Halsey's 3rd fleet on the 23rd and 24th. Losing Musashi, Atago and Maya sunk and Takao & Myoko forced to return to port. Following these attacks Kurita had started sailing away from the strait. This movement was observed by the Americans who assumed that he was retreating. Then after 5pm Kurita turned back around to his original course and passed through the strait in the pre-dawn hours of the 25th.

Meanwhile in the late afternoon of the 24th the Japanese decoy force commanded by Ozawa had been detected well to the north. Halsey pulled in his aircraft and charged north with the aim of eliminating the last Japanese carriers. Preliminary orders were drafted to create a battleship task force (TF34) to guard the exit from the San Bernadino strait but those orders were never executed before Halsey and most of the 3rd Fleet staff went to sleep. And that's where things get murky.

Kurita's change of course did not go unnoticed by the Americans. Night time reconnaissance revealed his progress and that information is known to have been relayed to 3rd Fleet. Indeed several senior officers in various sub-groups of 3rd fleet attempted to raise the issue with Halsey's staff but were brushed off and effectively told to mind their own business. To compound matters the commander of 7th Fleet (Kincaid), which was the superior HQ for Taffy 3, assumed that TF34 had in fact been created. If Kincaid had known that it had not been created he would have adjusted his own dispositions accordingly.

Presumably Halsey meant to re-examine his deployments on the 25th and create TF34 if needed. But by dawn on the 25th 3rd Fleet was hundreds of miles to the north^* and Kurita in Yamato was practically within gun range of Taffy 3. The rest is history.

source : possibly the best book about naval action in WWII, James Hornfischer's Last Stand of the Tin Can Sailors

^* Meaning that TF34 would have been useless at that point anyway. If it was to be created at all it needed to be created on the 24th before Halsey took his fleet north.