My best guess is that it's a debris effect from your ship taking damage, and it's supposed to fly away and expire, but somehow got stuck instead of disappearing, so now it's an "effect" on your character that doesn't know its supposed to have timed out already.
Other Bethesda games, especially Skyrim, had bugs like this of status effects that would get stuck on your character longer than they were supposed to and you'd only realize hours later when your character has some weird blue fog following them
It's not always the best option, like if you wanna save your gold for the ship upgrades it'll eat a big chunk out of that, but you could totally keep your gear perks that way if you really like them, you can upgrade at 61, don't have to wait for 62