Finding out about pet after tenants move out

[Josh Reighard]

Hello, I am just moving back to Chicago after living in NYC for a couple years. My yard had yellow dead grass from animals and my wife found pet cleaner. My Tenants were ideal overall but I am now finding out from multiple neighbors that they had a dog. Our lease specifically says no Pets. I don't have a fine or consequence in lease, just no pets. So far I have to replace sod/grass, have multiple scratch marks on wood floors, I am also considering an HVAC cleaning as I have terrible allergies, especially to Dogs/Cats. What would be best way to handle? I already have a list of things to charge our of security deposit. Is it fair to keep all of deposit or add on a pet fee? 

I have multiple properties in another state and have tenants with pets that we charge a non-refundable deposit and monthly fee. This is first time I have found out about pet after the fact. 

My father in law visited property for me a couple times over past few years and tenants always made it difficult for him to visit. Usually took a couple days and know it makes sense.