Playing Geneforge 2 right now and I just realized that I may have messed up my ending.
I'm going for the Pro Shapers ending, but I used some canisters without much thought and a message showed up when I visited a town. It said that people look at me with fear or something like that. My skin is glowing.

Did I messed up? Is my character going to die/get in prison by the Shaper Council?

Yes, I'm afraid so.

For the first Geneforge game (and possibly for the 5th, but it's been a while so I'm not certain), there's little functional difference in whether you choose to use canisters or not. In fact, in the first game it's encouraged.

After that, though, there are more serious consequences - particularly if you want to side with the Shapers, who do not approve of canister use. If possible, try saving your game (for a spot to return to) and siding with the Awakened faction. They don't mind canister use, as I recall (again, it's been a while).

Alternatively, you could try a cheat to reset the game's canister use count. WARNING: I'm not 100% certain about this one, so keep a backup save game. Even if it works, I'm not sure how the game reacts after you've gone through certain canister events. Once again, keep a backup save!

To reset canister use (for Geneforge 2, at least), try this: Shift-D (should bring up a console window), then type, without the quotes, "SDF 100 7 0".

There won't be any confirmation message or the like, so whether or not it works won't be immediately obvious.