Ah yes, the blinking light boxes. I actually discovered this earlier but didn't bother to fix them because I thought that nobody would bother to shoot them in the first place. (which shows you how lazy I am) However the ones near the Forest entrance do not explode because I thought that if any of them were to be shot it would be them, seeing as how they're the only ones between the Forest entrance and the Final Fortress. Later on however I added some more near the Forest Entrance Miniboss. (I'm guessing they're the ones you destroyed) No matter though, I'll fix them all in the updated version.
The save rings is a new one, thanks for informing me.
The doors can't be considered bugs. You'll notice that the only two doors I did that with (the yellow door leading to the centre of the Volcano and the yellow door leading out of the Factory) have flashing power lines emitting from them, unlike any of the normal doors. So while it's note immediately obvious that they're connected to a switch, it is clear that they have an extra ordinary feature.
As for the colours, is that really a bug? Is it? Nobody said anything about the brilliantly coloured scenery in Obstacle Course? Or the altered colour of the bugs and exotic forests in Temple Of Death?. And what about the brown walls in The Abandoned Factory? But yes you're right, the Ice Missiles, the Forest Roots, the shootable blocks that give you health and a great many other things are altered in colour.
Thanks for helping me weed out all the glitches though, I'll try to fix as much as I can in the updated version.