Could've been old damage that the previous owner never completely repaired. I've never done transoms before, but I imagine you'd be best off treating it like a hole and completely re-glassing the area, as much as possible. I guess it depends on how bad/large and where the cracks are. My local Hobie dealer just re-did some transoms on an 18, so it's doable, just gotta figure out how!
While kinda goofy, this guy explains everything you need to know to handle a basic fiberglass repair in his video series:
https://www.youtube.com/watch?v=i9hfpOCnzEs