Know your tenant laws and seek out a lawyer if necessary. Explain to the company your calculations, and if they aren't in agreement then tell them you will be seeking a lawyer regarding this. Print all of your evidence (check stubs, any rent receipts, etc) and be sure you have a copy of your lease! Also, if they never made an addendum to the lease, this sounds super illegal and shady on their part.

I had to sue an ex-landlord for withholding my deposit for various issues, that were a problem prior to my move-in and I could prove them without a problem. We settled before it went to court and she ended up paying over 3x my deposit in the end due to legal fees, etc for me going after her. I kept the letters she sent me, and sent her a letter via certified mail asking for my money back.