While looking at Alexander's campaign, I noticed that on his way to taking Persepolis, he was ambushed by a small Persian force lead by a satrap known as Ariobarzanes causing him to withdraw his forces and leave the slaughtered Macedonian troops behind. While he was eventually defeated after Alexander was told how to flank his army a month later, Ariobarzanes and his army forced the Macedonians to flee for the first time. Therefore, how is Alexander said to have never lost a battle? Is this because the fight was considered an ambush rather than a formal battle?
The simple answer is that it is not considered a defeat because Alexander did not lose.
There are different versions of the engagement in the 4 main surviving accounts of Alexander's life. The shortest is Plutarch (Life of Alexander 37.1), who says only that the passes into Persis were guarded by "the noblest of the Persians" and Alexander needed a guide to show him a secret way in. It would be pretty hard to spin this as a defeat.
Arrian (Anabasis 3.18), who is generally considered the best and most reliable source on Alexander, does not mention any ambush or setback either. He says the pass was blocked by a wall guarded by Ariobarzanes and an army of 40,000 infantry and 700 horsemen. Alexander's army approached it, lost some men to missiles, and withdrew safely. Alexander then decided to split his forces and led his best troops along a difficult road through the mountains to surround the Persians in the pass. When he was in position, his signal to the men before the wall began an assault on the hapless Persians from both sides, and they were quickly routed. While the operation took him an extra day, it only demonstrated his ingenuity and daring, against which the Persians could do nothing.
The story you cite of an ambush and serious Macedonian losses occurs only in the accounts of Diodoros (17.68) and Curtius Rufus (5.3-4). According to these sources, the Persian Gates (or Susian Rocks) were guarded by Ariobarzanes and a force of 25,000 infantry (plus 300 cavalry according to Diodoros). This army kept quiet until they had Alexander trapped in a narrow gorge, and then unleashed rocks and missiles on his marching column. The invading army had no choice but to pull back:
Alexander was quite helpless to avert the sufferings of his men and seeing that no one of the enemy was killed or even wounded, while of his own force many were slain and practically all the attacking force were disabled, he recalled the soldiers from the battle with a trumpet signal.
-- Diod. 17.68.3
If the story ended there, we might fairly call it a defeat for Alexander. But Diodoros specifically notes that Alexander refused to consider this the end of the matter and ask for his dead back under truce, because that would amount to an admission of defeat. Instead, he found a guide among his captives from the local population who knew a path around the pass. Led by this guide, he marched at night through the snow to get around the Persian force, and fell on their unsuspecting sentries at dawn. After the first few guarding units were broken, the rest fled the scene, and the pass was cleared.
Obviously there is quite a lot of disagreement between the versions of the story, and it's not clear which we should trust. But they all have certain features in common. They all say Alexander was checked on his way into Persis by a Persian army at a pass in the Zagros Mountains; they all agree that he could not simply advance and force the pass (whether he was really ambushed or not); they also agree that one of Alexander's prisoners was able to guide him along a difficult mountain path around the pass to strike the Persians in the rear. This way the Persian position was turned, the enemy army dislodged and the pass cleared. Alexander had incurred only a single day's delay. If there was indeed an ambush with casualties left in the pass, his men would have been able to bury them in safety.
There is no version of this story in which Alexander was defeated, any more than Xerxes was defeated at Thermopylai or the Americans at Omaha Beach. There may have been a temporary setback and some losses but Alexander gained an unquestionable victory the next day.