Ran into some issue with the amount of modules, where it is very hard to switch around what i want. Turns out if you cancel out of the module edit screen while you have a module in hand, it will deposit into the inventory, even over other items.
Can you explain the problem a bit? If a module is compatible, you can pick it up and click on the other module and it will swap the two. If I'm understanding correctly, the second behavior is intended, when you remove a module and try to exit module edit while holding it, it'll put it back into storage
edit: I think I know what you mean, fixed a related bug in the rc4 version.