Wait. WHAT!?
(I'm assuming you mean stage 3 (Kappa Industries) when you say level 3 instead of the third room on stage one.)
That shouldn't happen at all. Especially since there's no door coded to appear in the stage 3 miniboss's room (the door is already there, it's in the area above the arena which is only accessible when you kill the miniboss and scrolling is restored.) I never had a problem like that come up during playtesting. If more people report it, or if you can give me definitive evidence that the glitch does exist and that this is not just a one-time occurance (I need to know if it can happen again) I'll look into fixing it. (also have you tried killing yourself using one of the hazards before the miniboss to see if it fixed the problem?)
I went back to it again and no door appeared this time. I swear I saw one pop up and vanish again. Whether or not the ceiling openned up back then, I don't know. Probably. I think I had too much of a "game glitched, I'm stuck"-mentality in my head to even notice anymore.
I played the rest of what came after that and I've got to say, good job. Something that could be changed: Decrease the health of the level 4 Bubbly Clouds endboss. Should you die on it, it becomes a massive drag to fight without at least a few projectiles at the start. Something other than decreasing health would be having the stars appear way outside the effect of the Master Spark. The way it is now, you have no chance to even get half of them.