This 100% occurs even in the downloaded Windows version. My best guess is once you get past 8-9 bullet speed some projectiles don't count as landing. And its a lot more egregious once you reach 20 bullet speed.
For example, the fast red worm stages, you need enough bullet speed to hit the ones on the top half of the map, but regardless of your bullet speed any red worms that spawn on the bottom half you will endlessly miss. The red worm stages are by far the most dangerous levels especially considering the miss bug.
If you don't have Orbital Flames and/or the bouncing lightning attack, the red worms that spawn from the bottom will hit you regardless, a number of times. The adds that spawn from the bottom should move slower (if thats even possible to make happen) since its so much closer to your flame and hitting things in general when they are the bottom is where a lot of the hit issues occur.