I assume you're referring to his (also assuming this is still Madara) reaction when Kabuto showed him the content of the crate? I always read that as more of a horrified "How did you get your hands on that?" reaction born of disgust and shock rather than true fear. I'd be somewhat disturbed myself if someone showed me my own dead body which they apparently plan to resurrect at will.

If you reaaaally want some far-fetched speculation, perhaps that body has some special ~spiritual~ connection which could somehow affect his current state, and Kabuto is holding that over him like a trump card. I don't know, this development feels a lot more like a red herring to me than a truly game-changing twist.