In Honey, I Shrunk the Kids, Wayne Szalinski describes his shrink-ray as reducing the "empty space" in matter to make things smaller. Granting the central conceit of the movie that such a thing is possible, it does not seem to follow that this altered matter would be able to interact normally with unaltered matter.
For example, how would lungs made out of this altered matter be able to process full-size oxygen molecules? For that matter, even atomic interactions we take for granted like friction and non-permeability of solid materials could potentially follow bizarre and unpredictable rules.
Was this ever addressed in any of the other films? I haven't watched them all, having heard years ago that they were terrible :)