There are problems with input and output slots on the GUI creation.
The server and client sides are not synchronized, which causes many glitches including duplicate items in slots, "ghost" item that disappears after picking them up or not being usable in some cases and other similar bugs. This could be fixed by implementing a proper server to client communication and will be fixed in the upcoming updates.
This issue can be avoided by using inherited inventory of block and using block events for slot management instead of GUI events for slot management. This way, the data is stored and synchronized.
This workaround solves most use cases, so we are lowering the priority of this issue. The workaround will be doable from MCreator 1.7.9 new procedure system and in versions above.