My guess is the heat gun.

Could be, but if we assume the cypress was kiln dried it probably picked up moisture during the build. It would pick up the most moisture at the open end grain along the joint. Then it was planed and faired. My guess is that the heat gun drove the moisture out of the ends of the strips causing some shrinkage which could have pulled the joint open.

As long as one side is open any gap at the joint can be filled when sheathing and no loss of strength should result. The blemishes will not result in any significant loss in performance. So go ahead and get on the water and fix'em later as Nick and Ron describe.
Geo. C.