Well, what's done is done. Depending on how long ago people your residents moved in, you can mention to them that this fee is still on their account and you are expecting payment. Treat it as an oversight to start, then get more businesslike if they continue to ignore it. The $25.00 should be on their monthly statement if they get one. Otherwise, keep e-mailing them to let them know that they have a balance on their account, and that if a certain amount of time goes by without payment, late fees will accrue.
If your jurisdiction allows you to return insufficient payments, return the rent checks to the residents if they do not include the fee.
As for the resident who is talking about getting rid of her cat, call her bluff and tell her to do so. Say that she has thirty days (or whatever) to pay the full $200 or get rid of the cat. If she does neither, she would be violating the pet agreement one way or the other. People will always claim "You never told me that!" after they've moved in, so don't let it sway you.
From now on, if you are still willing to do payment plans of any kind, create an addendum that should be signed along with the lease stating that they are expected to pay the fee on a monthly basis of $25 per month, and if they ever miss a payment, the payment plan is null and they will owe the full remainder.