Bug: I got the first eye thing (one of six needed for the damage upgrade) in Library and then lost all of my lives. The eye was no longer in my inventory, but the eye did not reappear in the level in follow up attempts. I assume I was locked out of the upgrade.
I thought I was going crazy and maybe just saw things, but after beating the last boss I decided to reset the data and quickly get back to the library to confirm it is there. Hopefully I beat it in my first attempt now and don't lose it again.