Thanks for playing! We also discovered that bug and have uploaded a fixed version. You should be able to play all the way through to the boss now (I'm replaying again right now to make sure).
It sucks when you play for a long time and then it breaks, so I'm sorry that happened to you.
This was also developed for a game jam, so we ran out of time to balance the robots and upgrades more. But I definitely agree that they need more work. Thanks for the feedback!