This occured in 1.3 3x. However, when I reloaded I could not reproduce this error, and everything was back to normal (it was some kind of overflow error I guess). The game was started (and finished later) in the same version of the program. If it helps, when I had put the research slider or the capacity slider to 100%, it jumped from -1.5B to -1.8B.
My other concern is that when I kill my own ships for BCs and there are multiple ships in that square, I can do it more times than the number of ships I actually have because the "ship stack" doesn't seem to update immediately. A ship destroyed in this way should disappear from the window immediately. Similar odd things can happen with a stack of ships around a planet, depending on what is selected at the time.
I found that the reason for having two types of factories in my build list was because I stole manufacturing centers from the AI and skipped over all the others. When I reloaded the game this "feature" went away also. However, I noticed that it actually enhanced the game to have basic factory always available in the build list (especially for new colonies) regardless of tech level. You might consider putting this feature into future patches or testing it out. Expanding on that idea, making a checkbox for "show obsolete buildings" and allowing all older buildings to be built might be a feature as well (although I'm sure you've thought about that already).
