Thank you so much for your engagement with the game! It is NOT an easy game, especially when going for all of the bananas so I'm happy to hear that you were invested in it.
The glitches that occur are, as far as I know, related to the GBS 2 Beta 5 engine as opposed to a logic issue in the scripts. Many OnUpdate scripts are used simultaneously for enemies, camera, and other things. I believe that in running so many, some events are either skipped or even overloaded in the RAM. So while the logic is good, the design does not make the proper accommodations for this, though there was certainly attempts! Level 3 is actually a good bit different because the original layout triggered these glitches far more easily. However, it was still not enough to be totally glitch-free.
That being said, I had a blast getting all that I could out of the engine (even if I pushed a little too hard) and who knows? Now that GBS 3 is out and has all of its great features, it could be a good time to build out a game closer to the original plans.
Thank you again for playing and for your thoughtful post! I'm glad to hear that you enjoyed :D