I think water-based acrylic paints have poor adhesion in general, which can create masking problems. Water-based acryic relies on polymerization for adhesion, so it is less inclined to stick to surfaces and more inclined to stick to itself. Consequently, it likes to peel off in chunks. You will likely need a very low tack tape for masking them, and the longer you leave the tape on, the greater the chance of a problem. I rarely have a problem with lacquer based acrylics, which bite into the surface and will tolerate masking better. I've used bare metal foil with them, and the only nuisance is getting the foil off.
A good lacquer primer may help, or roughing the painting surface a little before applying the paint. Clear plastic has very little tooth for paint to grab onto.