I believe it has to do with once you turn into a frog you can't be turned back.

So, if the clone turns into a frog, then as soon as that clone "pops" naruto would instantly know "how" to turn into a frog (absorb the nature chakra without being able to control it) and therefore would himself turn into a frog since he is actively trying to absorb the nature chakra as well. Then it just becomes a problem of never being able to return to human form. I don't think it actually contradicts anything previously laid out.

The only discontinuity comes with the idea what if naruto isn't actively trying to absorb the nature chakra when the frog clone pops. In that case, he would still know how to absorb it without being able to control it so the next time he even tried he would become a frog (instantly would be my guess).