Roof sheeting is separating in layers... why?

You either have the wrong plywood sheeting or it has been exposed for more than just one rain. My shed has not shown any signs of lifting in over 4 months. Did you use exterior grade plywood or the cheaper interior grade. once it has started to separate it is going to continue as long as it is exposed to moisture. And there is an outside and inside surface marked on exterior plywood. See if you can nail it down to keep it from lifting any more before wasting a bunch of shingles

Depending on how badly delammed they are. I would either replace them or go over them with another layer. You may be able to just replace the bad ones, probably around the edges I'm guessing.

Plywood expands when it gets wet and then it cracks and peels with repeated wet and dry cycle. you need to make sure the plywood is well waterproof.