Could you share your code? Maybe your project? There's necessarily something missing somewhere, in your code or in the scene setup, but it's impossible to know what without more information.
I can't access the file. Could you make it downloadable?
Okay, it's simple, you never call code to transition back to the Idle animation in the tree. In Run.gd, you have
Which makes Mannequiny play the run animation.
You should also call this when entering Idle.gd: