Mouse Input for Build Mode Windows are switched

I'm making a multiplayer game which I'm currently testing by building the game and running one instance in the editor and one instance in the build mode window. For the multiplayer I'm using the photon engine where in the player controller script I simply test if the view is mine and then proceed to move the player. However I don't think the issue has to do with the photon engine. Now my problem is that whenever I click on the first of the two windows, the player on the second window gets moved by my WASD input. When I click on the second window the player on the first windows gets moved.

TL;DR: If I test my game in build mode and I click on one window to activate the view there, then the opposite player gets moved