Reaction with silicone possibly left on the playfield?
Reaction between the clear and the insert plastic?
Problem with this type of clear when it is applied in a puddle when filling the inserts? -- Are the ones that didn't bubble less cupped requiring less clear to fill?
Vid will know what to do, but I think you probably will have to sand away the bubbles once it drys. Then maybe try filling the inserts in a few shallow coats. Just some ideas I'm certainly no master.