Frogs can jump and squeeze into the tiniest crack sbut I'm a little surprised that they're still getting in if it's two or three feet above ground and you're using a cover. Perhaps they're just attracted to the warm water and can feel the heat from some distance away.
Short of covering the entire area with clingfilm or some other material which makes a completely airtight seal, I can' t think of any answer.. Have you tried contacting the manufacturers to see if this is a common problem and they can suggest a solution? I suspect though they might just laugh and find it funny. You might just have to arm yourself with a fishing net and long handle before you climb in. I'm surprised they're surviving. Arn't you supposed to put chlorine or some chemical in the water to keep it hygienic?