So I had lived in an apartment complex for about a year when I left about 2 months early for an internship. I paid for the next two months, so that isn't my problem. 

My problem occurred months after I checked out. My roommate and I had parted ways. They were going to stay in the apartment until the lease was up and I was leaving early. There were no problems but I did my final walk through with the landlord and everything was great.  She said there were no problems and that I have to worry about anything. I than wait for the next two months, while I was out of state, for my roommate to check out so we could process the security deposit.

They did the walk through and there were no problems and I called to verify. No problems. I then get a call about three weeks later stating that my roommate's room smelled like cat pee and that I was being held reliable. My ex-roommate hates cats and is slightly allergic so would always keep the door shut. My room which stored the cat litter and cat, had no smell. My cat is nine years old and I has never had a problem. I also didn't smell this when I did my final walk through and took my cat out of the house. What should I do?

Thanks

If the cat and litter was in the room then there is no way there can not be a smell. You may have been use to it and simply did not notice. There is no way that a cat will keep it in the box 100% of the time so there was likely a cost to eliminate the small. Whether it was the entire amount of the deposit is unknown.

First thing you do is ask to see copies of the landlords contractor fees for eliminating the smell. If the landlord did the clean up himself he is only entitled to charge you for material. He is not permitted to charge for his time.

Once you see the contractors fees you know what your landlord can legally deduct from your deposit.

Did you or your roommate sign a statement that said all was good at checkout? If so, refer them to that form. I don't know how they can wait three weeks to decide something is now suddenly wrong.

@Shelby L ilgenfritz That is a good point .. did this final walkthrough involve any signing off or paperwork

Yes, I did sign a paper when I left and it was all good. The room with the litter box didn’t have a problem and they are claiming the room (locked) with no litter box is the problem.

so send copy of paperwork back and ask for your full deposit as outlined in said copy of paperwork...

UPDATE!

I requested the paperwork. They haven't given it to me after a few days but I called them today and they said they would send it to me tomorrow via email. They also have completely changed their statement and have now replaced all the carpets in the apartment at my cost. They kept the entire security deposit, restoration fee, and charged me 1200$ extra. I, nor anybody else, smelled this cat urine. So I requested a 3rd party to inspect it, but they changed the carpets today. I requested a 3rd party inspection a week ago. I have a meeting with a lawyer through my university this coming Wednesday. Has anybody ran into a problem like this. The property manager told me on the phone that they ignored her request to just clean the carpets and opted instead to replace them. They did a walk through privately. She told me I was just young and naive and they had been in business a long time and knew better than me. I am also hearing that 7 other apartments in my complex are also having the carpets completely changed because of apparent cat urine... Note I moved out May 19th and my other roommate moved out before the end of June. We have had no refund and every time I call the conversation changes.

Most states award treble damages for unlawfully keeping a security deposit if you choose to go that route. However nothing is ever guaranteed if it goes to court. Your options are 1) ignore it, walk away from the security deposit, don't pay their extra fees. If they file suit then you fight it. 2) Sue them for unlawfully keeping your deposit. If you have the signed statements from both you and your roommate you should be in good shape. Make sure to bring the lease, proof you paid rent the entirety of the lease, and any other documentation. Read the local property code and file for the maximum penalties including lawyers fees if you use one. You could do this in small claims court yourself. 

I would lean toward #1. If they are a big complex they have been around the block and will know how to win. Maybe you could send some scary demand letter from a lawyer to hopefully deter them from filing suit against you for the unpaid charges but it is not a great situation especially since you are out of state. 

Lawsuits should be viewed as investments. Objectively look at the potential return vs risk before proceeding. Don't just file suits as a matter of principle.

Its tough to argue a smell in court . 

how old were the carpets?  Usually 3 years is considered their lifetime.  Landlord normally can't  charge you for replacement if this old.  I believe if they are replaced sooner their value must be prorated.   Regardless cats do stink no matter what you do and it takes time and effort to eliminate the odor.  This is why i never allow cats in units.

@James Moore You gotta know when to hold em and when to fold em ‘ It’s time to fold em’ Let the guy keep the deposit and don’t give him a red cent for that carpet . You never agreed or consented to buying carpet or admitting guilt . **If they file suit have an attorney send them a certIfIed letter and be sure it states that you have that signed final walkthrough document ready to use in court !

It sounds like a pattern of behavior, and the landlord/PM is abusing pet owners to cover their carpet costs.  I would take careful notes of how the story changed and send a formal demand for the return of your security deposit - I'd fight it for justice, but there isn't shame in backing away (and not giving them any more money) if you're not up to the fight.