How did Tommy get arrested at the end of the movie but not Rocky.

Gunn challenged Rocky to a fight, Rocky accepted and drew first blood(Couldn't help but throw in the Rambo reference)

The only thing Gunn could've been arrested for is maybe disturbing the peace

Tommy SOUGHT Rocky out and he - a professional fighter - assaulted Paulie: https://www.youtube.com/watch?v=xtrSAagZCUA. Plus, Rocky ended the Cold War.

Perhaps the police were called as soon as Tommy punched Paulie?
Plus Gunn also assaulted a couple of other guys during the bout with Balboa, and perhaps it was in connection to that?

You don't want to arrest Stallone...First Blood, Lock Up, Escape Plan, etc.

The last fight was changed in the final print of the film so I guess something must have been left out or they simply wanted to show that Tommy ended his career permanently by forcefully assaulting Pauli and other citizens besides Rocky and having the whole thing filmed by TV which probably justified his arrest.

Duke also warned Tommy that he should back-off and not start a street fight or his career is finished in the business.

That was the stipulation for the fight. The loser goes to jail. For some reason though, the scene explaining this was edited out

I started thinking this too. The only real thing I can think of is the assault on Paulie.

rocky is man of people. the cops know this and arrest tommy for his betrayal.