After the patch from bug 18805, the Total Due amount on members/pay.pl is total fines - total credits. However, if one clicks Pay Amount then members/paycollect.pl auto-populates the Collect From Patron field with an amount that is just total fines, not factoring in credits. I can see how this is technically correct and one would expect users to first apply credits and then take payment on the remaining balance, but members/paycollect.pl could still stand to be clarified in some way.
It's still the case: When paying the form prefills with the open debits, credits not included. This doesn't feel wrong to me. I am not sure how a clarification could look like - just a note hinting to the existing credit?