If Bomb Factory #2 is the one where you fight Meta Ridley, then I think I know which secret you'd be missing. After the fight sequence (with all the ROBs and Subspace bombs in the background) is when this happens. After a couple of falling rooms, you should come to a part where you are carried along by a scrolling screen. There will be a part where you run to the right and fall to a point where there is a enemy generator (the purple-ish circle). For a split-second, you should be able to see a trophy in the bottom right corner of this chamber. You should be able to grab it if the Mites aren't harassing you too much.
The secret I was missing from the Upper-Right Great Maze is this:
(sorry about this explanation, it's kind of vague)
There's a room somewhere XD that has a few conveyor belts. At a few places along the belts are metal boxes that hide what's behind them. They all have a billion million Mites pouring from them. I think it's safe to say that they all have enemy generators behind them. One in particular spat out about 5 stickers when I swiped at it. Just find this room and clear it out, you should find what you are looking for.
Hope that wasn't too much of a wall of text. Good luck getting 100%!
EDIT: Okay, I forgot the other one for the bomb factory that is likely to be missed. The first door that you find in the level (on a moving platform while the level is scrolling a bit) leads to an optional room. Use the spring to leave the top of the screen; there is a box there (completely hidden from view, mind you)
