I haven't read Gladwell's book, admittedly, but I can speak to an illustrative case that I've studied well, the American bombing operations in Romania between 1942 and 1944.

The short answer is yes, in many cases the bombings were quite inefficient, for several reasons. The concept of strategic bombing was still in its infancy, and there was quite a bit of disagreement over the "proper" way to do it; e.g. daytime precision bombing vs. nighttime bombing. There were also practical issues related to the ability to accurately target bombs given the state of 1940s technology.

Looking specifically at the case of the American raids in Romania, Romania was of course Hitler's main source of crude oil, providing somewhere between a quarter and a third of Germany's oil during WWII. The Americans wanted to bomb the Romanian refineries to shut down Romanian oil production (at least temporarily), in coordination with bombing efforts against other targets like German synthetic fuel plants as part of an operation known as the Oil Campaign.

The initial problem the USAAF faced in bombing Romania early on was the lack of airfields within the range of the planes that were in use by the Ninth Air Force at the time, the B-24 Liberator. The first attempted raid against Romania was the so-called "Halverson Project" or HALPRO raid on 12 June 1942. This was a small raid with just 13 planes, more of a show of force than an actual strategic bombing mission. They took off from Egypt and dropped a few bombs near the main center of the Romanian oil industry in Ploiesti, and a few others in other locations. The damage was pretty trivial and of no strategic significance. Well, for the Americans anyway. The Axis recognized that the Americans were capable of bombing them and installed massive AA defenses around Ploiesti, making it one of the best-defended targets in Europe.

The bigger and better known raid, and the one that demonstrated the limitations of strategic bombing in WWII, at least in that theater, was Operation Tidal Wave on 1 August 1943. This was a much larger operation (over 150 planes) that was intended to do serious damage to Romanian oil refining capacity. This time they were flying from Libya, which is still a long way away from Romania obviously, but a bit closer than Egypt. They lost something like 15 planes to mechanical problems before they even reached the target, and the bombing groups got separated after one group made a wrong turn, ending up near Bucharest instead of over the targets at Ploiesti and Câmpina. They didn't want to break radio silence and alert the German and Romanian fighters (which didn't work, they were detected anyway), so they ended up hitting the target areas piecemeal instead of in a coordinated effort. They also used borderline suicidal tactics, flying in only a couple hundred feet above ground in an effort to avoid German radar, which made them sitting ducks for the heavy AA defenses. Most of the planes ended up delivering their payloads near their targets (although some planes got lost and hit targets of opportunity instead), but the combination of disorganization and effective resistance meant that the damage to the refineries ended up being relatively minor and didn't do much to curtail output at all. The US lost over 50 planes and lost 500 men killed or captured for very little return.

Once the Allies had advanced northward into Italy in 1944, the American and British air forces were able to launch raids on Romania from there, using more normal tactics. The first bombing of Bucharest was on 4 April 1944, mainly targeting the railyards since that was one of the main transfer points for men and materiel headed to the Eastern Front (where the Soviet spring offensive was reaching a stalemate). They managed to inflict some damage on the rail lines, but a lot of the bombs were blown off target by the wind and hit civilian targets, killing over 5,000 civilians (according to the official Romanian figures). There was another bombing raid against Ploiesti in June, which was a dive-bombing attack with P-38s. This operation was also unsuccessful. So in the end, the Allied operations in Romania ended up achieving very little in a strategic sense, due to logistical problems, poor strategy, and technological limitations of the equipment at the time.

I assume you were asking primarily about bombing of Germany and Japan, which I know less about and haven't done research on. Romania is the only area I've actually researched myself, so I figured I would chime in with that. It's a small sample size of relatively unorthodox operations, but it certainly demonstrates some of the limitations of strategic bombing at the time.

Sources:

Jay Stout, Fortress Ploesti: The Campaign to Destroy Hitler's Oil (Casemate, 2003)

James Dugan and Carroll Stewart, Ploesti: The Great Ground-Air Battle of 1 August 1943 (1962)

Duane Schultz, Into the Fire (Westholme, 2007)

NARA II, RG 389 - Timisul de Jos [Records of interviews with former American prisoners of war in Romania]