Thank you for taking your time writing this down! As you can see from this comment thread, I try to answer every question there is and take all the feedback very seriously. Some comments of mine have a bit more deeper explanation to what's going on though.
Everything "wrong" with the game pretty much just comes down to running out of time with so many things, like you mentioned, doing this completely solo and for the first time. I will update the game jam version here on itch.io to a "definitive version" with bug fixes and balance to its version after the jam's voting is over, which will be free to play for anyone. After that I will focus on getting it into early access on steam in a couple of months, with much much more content, polish and quality of life improvements. Expect a lot more easter eggs and achievement hunting, which you seemed to like, my fellow explorer. :p
The bugs you listed are already known to me. You hopefully won't enounter them next time!
Would be great to see you back with the game's first official update.
Edit: One thing to mention with the upgrade system is, that almost every upgrade scales virtually infinitely. e.g. you only get "Spread" and attack speed and this happens: a screenshot