I have had the same problem at times. None of the suggested cures worked for me. I have some planes that turned out perfect. Not one wrinkle or pucker. Then, they show up on the next one. Something in the process goes wrong at times and I have not figured it out. At times, the puckers appeared after three or four coats of dope. There were no puckers after the first coat or two but after that, they appeared.
Since dope softens the existing coats I wonder if the polyspan, or whatever covering, is pulling loose a bit when subsequent coats are applied. Also, polyspan is stronger span-wise than chord-wise. Is is possible that the shrinking due to heat and due to the dope is causing the polyspan to split, thus causing the puckers? But, why only where the caps trips meet the LE and TE? One batch of polyspan I have is pretty lousy. It looks to be a clone of the Starline product. This clone has rather large, thin areas that would never fill with dope. The weave is pretty light and it tears very easily in the chord-wise direction. I will not use it because of this.
I also wondered if the capstrips were moving, that is, rolling a little, due to the shrinkage of the covering. I have done the partial sheeting of foam cores with the capstrips and the capstrips should be more secure since they lay flat against the foam. But, the puckers still appear at times.
The project I have in work now is partially sheeted foam with capstrips. I started this one long ago and put it aside to do other projects. It is worth finishing and I will cover this one with Thermal Span, which is like polyspan but just as strong chord-wise as span-wise. We shall see if this makes any difference.
All future projects will be fully sheeted. I have found little difference in final weight between fully sheeting and conventional covering. It is much easier to finish out the wing if fully sheeted so I am taking the easier path.