I recently came back to the game to 100% the achievements, and after finishing a no-upgrades playthrough, I went back around the map to collect everything that I'd skipped. In the end, I saw that I had a blank spot in the upgrade station list, which I figured out was the Shield Dynamo upgrade. I checked a walkthrough, and I definitely opened the upgrade box containing that power-up; it's sitting there empty, but I don't have access to the upgrade. Seems like I somehow managed to erase it from existence. I was doing a lot of quitting to the main menu and reloading during my playthrough, to keep my death count under 5 and get the achievement, so maybe I triggered some sort of state bug. It's not a big deal, since I've already 100% the game on another save, but it's still weird.