So I checked out the update and can confirm that the upgrades disappearing issue I mentioned is actually limited to the 3D printer (and maybe inventory items?).
If you die or reload a save in any way then you can't repair the ship with thrash anymore, the only way to fix it is to get a chill point and get another upgrade, though it happens again next time a save is loaded.
After that bug happens the 3D printer also doesn't show up in the inventory menu anymore, same for the trash, though that could be just a visual thing.
Also ran into an issue with the item you find in one of the asteroid areas (the nav computer I think?), when I picked it up it would break the ship menu's camera and dialogue menus, making them almost unusable.
I didn't pick it up because of it so if it was needed for the main quest then I might be softlocked now.
Fix is up for both issues (1.0.9). Thanks a lot for the investigation, it helped me locate the bug quick!
Not taking the nav computer shouldn’t soft-lock you, it should just keep reappearing if you use the Sector Scanner until you pick it up as it’s necessary for progress. I’ve drastically reduced the amount of post-processing it applies, so it should now work both in new saves and any old ones where you already have it.