I think I figured out one of the biggest reasons for my issue which is squeegee technique. I've been holding it at too shallow an angle & so even pushing with two hands wasn't getting all the solution out from under the film. Gel is more pronounced because of it's viscosity. Holding it at the proper angle and overlapping swipes has virtually eliminated the issue.
Lesson learned.
Still wondering if the gel pockets will dissipate. Pic is typical of the size.