Depends on the size of the intrusion but theres many things you could use. I like that Magic Putty stuff but a product sold at hardware stores by Loctite is awesome and cheap. It's dark blue and white. Like 3 bucks a tube.

Or some good old fashioned roof repair stuff in a small can. Even some weatherstripping glue for that matter if it's a small crack or whatever.

 

non -self leveling polyurethane caulk in a tube ,someone who knows how to tool a caulk bead,awork platform to work off of .try to keep the weight off of the metal roof exspecially if the box is made of thin aluminum .It is like trying to reseal a old camper .Dip your finger in a dishsoap/water solution before tooling with finger and couple rags handy.a experienced caulker is most important .