Sounds like you can't afford your pets. Rehome them ASAP so you can ensure they land in a good home and you're not stuck putting them into an animal shelter when you are evicted.
If you get assessed a late fee for one month's rent the payment to cover it typically comes off the top of your next payment. As an example, suppose your total monthly rent is $700, which would include all pet fees, and the monthly late fee is $50.
Month 1: you pay late but do eventually pay the $700 in full. You are assessed a $50 late fee (total $50 owed).
Month 2: you pay $700. The prior month's late fee would come out of that first, so in reality you paid $650 in rent. You will get assessed another $50 late fee plus you still owe $50 for the unpaid rent (total $100 owed).
Month 3: you pay $725. The back rent plus late fees for the prior month come out of that, so you paid $625 in rent, you still owe $75, and you will get assessed another $50 late fee (total $125 owed).
See how it works? Now go back from April until now, using your monthly rent and late fee values from your lease, and figure out how much you owe the landlord, if anything.