Step 1: Open the itch app
Step 2: Quickly launch any game that has updated since the last time you opened the app - you have a 30s+ window to do this
The app will then attempt to update the game while it's running, replacing some files but failing to replace others because they're in use, resulting in a half updated amalgamation that will probably break the next time you try to run it if not immediately.
The app needs to ensure that a game isn't running before it tries to update it to prevent issues like this.