Think about it. Jon supposedly had Henry and a cohort in the hotel room with the police keeping watch outside. Jon shoots Henry's partner in the knee to shut him up for being sassy. Jon makes his ultimatum to Henry and Henry shows Jon his throat, backing down from confrontation with a major major trafficker.

Next thing we know, Henry and Jon meet up again. Henry asks Jon to come with him to look in the trunk of his car. The guy Jon shot in the knee is in the trunk, whacked by Henry.

This story is believable because it's logical. You see, Henry had to kill the guy Jon shot in the knee so that he wouldn't squeal on him to the Mafia back in New York. Henry is not supposed to be hiding Jon's whereabouts from anyone. If the New York mafia heard from anywhere that Henry visited his "friend" Jon down in Miami, and Jon was a marked man to begin with, Henry would have been killed by the Demeo crew right away. So the guy had to go.