Funny Bugs and Post-Jam Jupiter II
At some point, the mysterious bugs and great ideas from feedback I've gotten for Jupiter II caused me to roll a post-jam version. This version includes very important content such as a 100% aesthetic diving cable which took hours to get to look right.

You can find links to the post-jam version (both for Windows and HTML5) on the Jupiter II Ludum Dare Page.
The Case of the Frozen Fishsticks Solved
One of the major bug mysterious that was solved was the case of the fish and jellyfish seemingly spawning inside the ice walls. I double and triple-checked my math and code, and by all accounts it shouldn't have been happening.
Well, it actually wasn't happening, the spawn code was working just fine. What was happening, however, was my digital animals apparently trying to escape the matrix. I finally decided to increase the resolution and zoom the camera way out to actually watch the spawning happening (something I should have tried during development) and I witnessed what was going on.
The game spawns the tunnel below the player in chunks as you go deeper, and erases chunks and entities that are above you. Creatures are spawned in along with the chunks inside the new section of tunnel. The problem was that creatures are active as soon as they spawn, swimming around and whatnot even before the player is close. I finally saw that the little buggers would sometimes swim out the bottom of their chunk into the void where a future chunk would spawn, but there was none there yet. Then, when the player reached a certain point, a new chunk would spawn, and any fishes out in the void where there used to be no chunk all the sudden had a wall pop into existence on top of them.

In the end, the code was working just fine, I just hadn't considered the subtle implications of everything that was going on. I'm happy to have finally tracked this bug down, even if it was post-jam. I thought it was pretty funny and wanted to share.