I had something like this happen to me once on a 13 foot canoe. I figured it was caused by the canvassing technique I was using at the time.
As I recall I canvassed & mudded this 13 footer in the late fall, and first noticed the wrinkles a few weeks later as the temperature fluctuated down. The wrinkles seemed to come & go. I figured it was triggered by the temperature change. Now, back then I would stretch the hell out of the canvas, then after a few hours I would start at the center of the canoe and use the canvas stretchers along the rails, pulling & stapling my way to the stem area. I then would remove the canvas tension and attempt to staple along the stems. Of course the canvas would relax a great deal when I removed the tension, especially by the stems. So I would have to pull the canvas tight again as best I could at the stems, stapling as I go. But at the end I would inevitably have new wrinkles at the rails, so I had to remove the staples, pull up on the canvas again and re-staple.
This technique had worked ok for me before for longer canoes, but I figured it was inadequate for the 13 footer, and I fugured it was due to the canoe's stubby shape by the decks. My guess is that when I was done canvassing the canvas fibers were no longer as 'straight' as they were when the canvas was stretched due to all the re-work I had to do to remove the wrinkles that appeared along the rails after I was done with the stems.
So I changed my canvassing technique. I still stretch the canvas like hell for a few hours (when I use canvas). But before I start stapling I remove some of the tension to let the canvas relax a little. Then I use the canvas pullers along the rails to stretch 'up' along the rails as normal (I figure this is made easier & more effective by the relaxed tension). But then I add some staples along the outside of the stems at about 3" or 4" intervals (these will be removed later). Then I remove the tension completely. Then starting at the top of the canoe I staple & trim the canvas by the stems as normal, but the process is now much easier because the staples I added to the outside of the stems are keeping the canvas in the same position (more or less) as it was when stretched. These these side staples are removed as I work my way down to the bottom of the canoe.
Never had wrinkles appear again. Not sayin' this was your problem though...