My mother has been living in AL for 1 year and is now having problems with pets at the facility. Does anyone have experience with this?

My understanding as an activity professional dogs fit into these categories:
Service Dog - this dog I able to go anywhere the owner goes and it is no longer allowed by law to ask the owner for proof of being a Service Dog. The Service Dog is trained for specific tasks for a specific individual and should not be wandering into others rooms. It should also be leashed.

Therapy Dog: A Therapy Dog is a dog that is well-trained by professionals and can visit from room-to-room however; it is standard protocol for the owner to ask each patient if they would like a Therapy Dog visit. They should not be off a leash when around patients and should be highly trained to respond to directions.
Having a "Therapy Dog" in and out of an office area all day does not constitute what the intent of a therapy dog is for.

Comfort Pets: Comfort pets are NOT protected by the same guidelines as a Service Dog. “Comforting” or “giving love”, although clinically proven to be beneficial for people, is not acknowledged as a trained “task” by the Department of Justice, which enforces the ADA. (Is a ‘Comfort Dog’ a Service Dog?By joann_turnbull on February 21, 2009 at 7:00 AM).
The so called Comfort Dog" should not be allowed in food areas or patient rooms and should be with the owner in his office only - if in fact he really needs it there.
My guess is you hit the nail on the head. The owner thinks he has found a way to have his dog at work daily. You could call the health dept and ask them to do an inspection.
The down side is that you can register your dog online and get real cool looking credentials that really mean nothing. If someone says this is a comfort dog it is not allowed in a restaurant, theaters, etc. Unfortunately we are seeing more Service Dogs because the ADA states you can not ask for proof of the task so once someone says " this is a "service dog" it can go anywhere. It should also be leashed.
Good luck and you have options. Contact local agencies re: this pet in food areas and regarding misc. pets of leash as well. It should not be happening unless it is in a specified area with the owner only.