I'm not sure how many other single-players out there use the pause option as frequently as I do so this might not be a big problem. But I did notice that when you have paused the game and are in the research tree ordering several items, the game lets you pick more than you can really afford, and only de-selects the ones you can't afford after you un-pause.
Say you have 1000/100/100 money/metal/crystal and you pause the game and order a 400/0/50 research item. The totals in the upper right now show 600/0/50 (which is correct), but you can STILL select a second 800/0/75 item! The game doesn't gray that selection out like it should. Select that item and the totals in the upper right will show -200/0/-25, which is kind of flaky and neat at the same time. Then when you unpause, the game automatically DE-SELECTS that second research item because you couldn't afford it. (The same problem does not occur when you queue up ships to construct.)
A couple times when I wasn't paying attention, I paused and queued up some research only to find out later that it didn't happen because the game automatically removed it from my queue.
I'm guessing this bug occurs because you could afford it before you paused the game and although it refreshes the money/metal/crystal DISPLAYED when you're paused, it doesn't refresh the numbers that are used in the "can I afford this research?" logic.
(FYI the reason I use Pause so much is NOT because I have a small bladder. It's because I get so sucked into watching fleet combat actions that I often forget to go elsewhere and multitask, so I say "Oh yeah! I'm PLAYING this game!" and freeze it so I can queue up a lot of orders and stuff, and then go back to watching frigates get chomped. )