Ah, another B-17 fan!! Hmmm... how long has the BMF been sitting on the canopy? it's either that or you burnished it down a little too well... You might want to try to
gently wedge a #11 Xacto blade under there to help peel it off. Be careful not to scratch the canopy, though. If I remember correctly, you can get rid of the adhesive residue with a cotton swab dipped in acetone. becareful here too because acetone will eat away at some paint.
Hope this helps. Oh, what scale B-17 are you building? E, F or G model?