[ THE FOLLOWING TEXT IS SAVED FOR ARCHIVING PURPOSES. IT HAS BEEN SOLVED. NO NEED TO ANSWER ]

I am experiencing multiple problems regarding hatches and connection points. I am building a stealth weapons bay with these angles. Every time I nudge the whole assembly into the fuselage, it binds the connections into the fuselage itself. I.e the doors that should only connect to the hinge also connects into the fuselage.
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Anyone else has this problem?

Edit: [ FOLLOWING STATEMENT IS RENDERED USELESS ] Apparently this happens because I was checking the connections using that tool. I think it works by checking the surrounding parts and if so, it reads those possible parts as connected since it’s near. But since it is read as connected, the system now resets the connections and follows that all of those near parts as actually connected

To solve this, assuming this is true, is to NOT use the parts connections tool

Edit2: Apparently the tool isn’t a tool that checks connection, but reconnects parts.

Whoops.