I know it's poor form for a developer to say, "it's meant to be that way", but... it is! The theme of the jam was "glitch", so the puzzles of the game revolve around it breaking in various ways.
Sadly, there's no devlog; but if you want the quick story: far too many late nights and a design that was mostly composed of stealing bits and pieces from other games. The Metroid series is, of course, the main influence, with the ship's computer being a bit of SHODAN and a bit of GLaDOS.
Thanks for playing!