I am the sole home owner after a recent divorce. The town has sent me a letter stating I am running a rooming/boarding house. I have 2 room mates, that needed a place to stay and I had 2 spare bedrooms to let them occupy, am I not allowed to have room mates?

Yes you are allowed to have roommates. I suspect that your ex is out to get you.
Go in person to the town department that sent the letter, first to make sure it came from them, and second to see what grounds they are using. I doubt that there are any 'cohabitation' laws for 3 unrelated people, and many towns that had such laws in the 60s and 70s had to give them up because they were deemed unconstitutional. As long as you all share the same common areas, you are all roommates.
Make sure there aren't laws about number of cars, etc.
Keep in mind that the rent they pay you is considered income by the state and feds, and your ex may next turn you in for that...