Sometimes Unity "skips" or "stutters" when you switch to/from it while playing a game inside the Editor. I've seen this happen a lot, as well, and unfortunately there's nothing that can be done about it. You should file a bug report with Unity Technologies if it persists, though I'm sure by now they already know about it and are working to fix it (if they haven't already).
Fortunately, this has never happened to me while playing the game as a standalone built EXE, it only happens in the editor. So don't worry about this bug in your final-built game, it shouldn't happen.