The most common manifestation of this bug is that a player's frigate queue gets bugged with extra/phantom frigates that never finish construction and apparently tie down funds. I've also had the bug happen to me with the research queue, e.g. the repair platform can get "double researched" with funds taken twice for it.

 

When one of these phantom orders happens, typically some of the displayed savings counter go negative (unless you had lots of credits/resources beforehand). A more certain way to tell when the frigate build counters get bugged is to compare the top-level counter with the detailed sub-panel counters. In the screenshots attached (http://imgur.com/a/55L4f -- use the full resolution version by clicking in the upper right corner), you can see that (at the same paused moment in the game) the top-level counter is 2, while in the sub-panel there appear to be 3 queued frigates, one of which is a phantom order that will never finish. You can also see in those two screenshots that the credits savings counter went negative (because of the phantom order.)

 

For quite a while I thought that the negative savings doesn't impact gameplay beyond a UI nuisance, and I thought this because when playing back a recording of that "bugged" game the savings never go negative and the phantom orders never show in any queue. However, much later on I've noticed that the negative savings do affect the game engine's idea of what you can build. In the second pair of screenshots (same url as above) you can see that at the same moment in time, (but later than the one in the first pair of screenshots) I can't build any frigates for lack of funds, but I can build repair platforms. Since a Cobalt is cheaper than a repair platform on all three costs, this situation shouldn't ever happen... but it does once the game's econ gets confused.

 

EDIT note: I've changed the report above with screenshots instead of a save game. I'm not sure why thought I managed to capture the bug in the save game I posted initially because when I loaded it later, after restarting the dev exe... the bug's effects went away. So the bug doesn't seem to be capturable in a save game. Or to put it another way, a save+load will clear this bug 95% to 100% of the time, which is a reasonable workaround except that it prohibits a single continuous recording. The bug alas never clears out by itself otherwise during play and after enough continuous play time it accumulates phantom orders of all kinds (multiple frigates, research, even planetary upgrades.) It seems to me that the likelihood of this bug happening is directly proportional to the number of clicks that a queue normally sees, so the frigate queues are the one most likely to get hit by it early on. Also, the obvious potential workaround of right clicking to cancel those phantom orders doesn't work; the phantom orders don't get cancelled, but the real ones do...