Steps to reproduce:
1) Create an item prototype and add a application prototype named "0".
2) Save changes.
3) Open an edit form of same item prototype.
4) Observe that there are 2 selected options in the list of application prototypes now: "None" and "0".
5) Select "0" as only application prototype for particular item prototype.
6) Save changes.
7) Go back to edit form and see what happened.

Result:
Application prototype "0" is now deleted and "None" is selected.