This often happens when you have preprocessing software/applications watching the project, such as Prepros or Codekit. Also, Atom and Sublime (and even Notepad++) can cause this to happen if a file in the project is currently being edited.
The easiest way around the issue is to close whatever has the project files open, merge your branches, and then re-open them to refresh it. This will also avoid any problems where the program is no longer aware of any changes that have happened, forcing you to refresh the project(s) by hand.