It's because the 'damage' part of the shot is activated after a short delay. If an enemy moves fast enough, it can be hit by the projectile and move out of the way during the 'damage delay'.
You can see this a lot with Devilites. They get 'hit', dodge, and evade all damage. If a rebound bullet flew out at the Devilite's original position, you have yourself a 'dud'.
In rare cases, if you aim extremely closely to a target without hitting it (when aiming to the side of a target), the bullet will play its contact animation without ever having touched the target. The actual bullet will be invisible, ghosting past what it looked like it hit, still able to land a hit on something else.
You can see this more often with Skellies, or other slow/stationary foes. I'm pretty sure it only happens with basic shots, not rebounds or charged shots. If it does happen to those as well, I've never seen that happen.
So, uh, yeah. I hope it gets fixed myself. Just wanted to shed some light on things.