NCIS used to use my English department building at University as their Hospital. Star Fleet Academy in one of the Star Trek movies was the front of my school's library.

Considering how much they did there it wasn't nearly as inconvenient as you would think. The school had a good process in place for controlling the chaos. It's still weird watching the movie and seeing my old library in it.

Shooting in Baltimore for a story that is about Baltimore is different than shooting in a different city as a stand-in for the city in the script though. That's just normal location shooting.