Leaving aside the obvious explanation of conservation of ninjutsu, there's also what we see of the training in the series. I don't recall any sort of psych evaluation or training to help the soldiers better cope with the sort of existential crisis that comes along with fighting inhuman monstrosities that exist (apparently) solely to eat you and everyone you know. That, and in the training montage episodes they apparently don't train in small-group tactics, but rather compete for the kills, as in the combat exercise in the forest with the dummy Titans. They aren't preparing their soldiers for the shock of seeing friends and comrades killed and eaten, and they aren't training them to work together as a cohesive unit.
That, and with a few exceptions the most skilled recruits are also the farthest from the front lines. This exacerbates the issue by removing skilled fighters from the battle. Their front-line soldiers are a combination of the borderline-suicidal recon corps, composed primarily of those who are lucky enough to live long enough to become skilled fighters, and the wall guard, composed primarily of the mediocre recruits (who have apparently not been taught even basic squad tactics).
They don't fight as cohesive units, they fight as individuals. They are more warrior than soldier, and in a situation where combat is a very high-risk situation, most aren't going to live very long. That leaves aside those who abandon their posts to hide, and those who do the same to blindly attack. When they engage a Titan or group of the same, they all charge individually and swarm them. It doesn't explain everything away, but it goes a long way.