Cutting at Day 54 isn't necessarily bad (I do it), but you don't want to force them to come out of the egg unless you can see a problem, or one is taking many days longer than the others in the same clutch to come out (which could indicate a problem). This clutch shouldn't bother any other eggs in your incubator, as long as it is in its own, enclosed, egg tub. Oh, and throw out the bad egg if it isn't attached to the good ones.