Ahah, that startup effect!
My biggest gripe with the game is the fact that I need to click stuff between levels, so I guess you did pretty good :D
The second one is that sometimes, objectives and pressure plates are too close, and you plug the thing by accident, and because you can't unplug it you have to reset the level.
There are some weird control things that aren't really important but still there (the walljumps, or the fact that you can't jump at the start of a level for a while). And I think the difficulty curve could have been better. You introduce new mechanics in simple puzzles, but things could have been mixed a little better I think.
Oh and like kwis said the hourglass sound is really bad (mainly loud).
Anyway, still very good overall!
EDIT: I didn't meant to say bad as badly made, but more like it doesn't really go well with the fact that it's a bonus. I'm not sure how to explain it, it kinda sound "aggressive", I guess.
And yeah so, I relaunched the game because one frame shouldn't be noticed. It made me realize that the levels didn't start until you pressed something (at least when restarting a level with R). So if you start by pressing a direction you don't notice that, but if you start by jumping it activates the level but you don't jump. So I guess that's what felt like jumps not being registered, because we started levels by jumping.
Also, since I restarted the game, the player should have a way to skip the intro :D