I’ve encountered a very strange bug in Unity 2.6. Whenever I make a modification to a script, it cause the game to pause. For instance, I had an animation that was triggered by the button “Fire1”. I added a line of telling the animation to rewind, and whenever the rewind was attempted, the editor would pause the game and refuse to unpause it. I also tested it by writing a new script from scratch, with the same effect–the moment the game used the script, it froze. As far as I can tell, and changes in code/new code is causing the editor to pause the game. The error started very randomly, and has not changed after restarting the program, or restarting the computer. I have not seen if this problem persists with other projects or just this project.
just to be sure: do NOT leave the game in play mode while modifying the script unless you are seeking an undefine game state or more commonly flat out crashes of the whole editor!
as for the pausing in general: open the console window and check if you enabled “pause on error” and see if you got an error 
Ahh, that’s it. It was pausing on error–the strange thing is that it didn’t return any sort of error on the console until I unpaused it.
that indeed is strange, normally the error hits you before the pause happens.
I am having this problem but without modifying any scripts. When I set it to pause on error it pauses on the expected error, and then cannot be unpaused or stopped. I also cant close the error window. The main menus and the inspector are still normal.