Something I found that may or may not actually be the case, but worked on all 9 of my runs yesterday:

Frye seems to be averse to dropping both a green AND a purple in the same spot. It didn't happen a single time for me yesterday. So what I did was immediately move my guys INTO a green spot (since they have green immunity). The green circle stays around a bit, and for me it is enough to last the whole fight.

If this is not actually the case and I just had a run of good luck I appologize, but would be worth checking out if you are having problems with the puddles.