Any time I add animations transitions multiple scripts stop functioning correctly, however on restarting Unity after saving, everything works correctly.

unity version: 5.4.1f1, present on 5.3.1f1 aswell. OS: Windows 10

I would appreciate some help as this is baffling me.

I am simply adding a transition in the animator between animations (walking to running). However as soon as I add a transition and test the scene in the game view, multiple scripts go wrong although no immediate error messages popup:

For example, I have a script that makes the camera follow the camera, this ceases to work and focuses on a static point, yet no errors show up.

Another one is that I have a script that governs the hotbar hud, and while it initially throws no errors when i try to select something in the hotbar (i.e. by pressing "2") it then throws a null reference error.

Now both of these would indicate I am doing something wrong, but if I save and restart unity, everything works as intended. Needless to say, restarting any time I fiddle with my animation transition isn't ideal.

Any help would be appreciated. I have no idea how to bugfix something that fixes itself on restarting unity.