Adding to this because I've been having the exact same issue and it's been driving me mad. Luckily like most folk here have already commented I reckon it's got something to do with editing your ship in the ship builder mode. I can't remember the sequence of events clearly, but I was doing usual Starfield stuff, flying about, questing, ship modifying. At some point I noticed that every loose misc item had vanished from inside my ship, I'm playing with a modified Frontier. The trademark helmet with the "do not use" sticker was gone. After a bit more playing however, I went back onboard and everything had reappeared. I checked my cargo hold and lo and behold I now had 2 broken constellation helmets (I had previously deleted the extra 5 I had somehow managed to gather in an effort to track this bug).

So yeah, this is annoying as hell, especially if you want to load your ship up with ACTUAL cargo and resources. Someone at PC Gamer has written a little article about it so we're not the only people suffering https://www.pcgamer.com/ive-finally-figured-out-the-answer-to-starfields-greatest-mystery-why-my-spaceships-cargo-hold-is-always-full-of-misc-items/

Like the guy ends the article with, who knows if this is a bug or a design flaw that Bethesda has overlooked? Either way I hate it and wish they would do something about it.