its ages since I've seen the set up but its usual for one of the bolts to be long with a split spacer that's meant to move a little in the alternator lug. The idea being to have the other 'lug' fitted snugly to the bracket and the spacer then takes up the space left using the long bolt. I'm not sure if that makes sense! There is an order to assembly.
Of course none of this helps you to get it off though! but perhaps explains why you have an over length bolt on one side.
