Alright so this is a weird bug. What happened was that I created an army on a cruiser using the build menu without forming an army before. Thus far everything is fine. I then right clicked on that cruiser with a couple of other units thus forming an army and this is where things get weird. I could no longer select the army normally. It would select the army but would display something else as being selected such as the central building or a power core.

This in itself is weird but what was weirder was that I also had this little X saying "Double click here to delete this unit" which I then promptly tried ( at this time I had the army selected but the selection showed a power generator) this lead to a CTD without any sort of error.