I was in engineering and selected to build a hunter. Nothing happened, so I clicked a few more times. I finally realized that I did not have a garage, so stopped clicking.
I clicked the geoscape button and time whizzed by.
An alien craft appeared, but the game did not pause or give a notification. I hit space bar and tried to click the craft, to no avail.
Then I clicked on something else, I am afraid I am not sure what (perhaps the launch interceptors button, or a base icon) and the "no garage space" notification came up. I cleared it, then it came up a few more times (because I had tried several times to build the hunter. What do they say about trying the same thing and expecting different results?).
After clearing the hidden messages an "alien craft detected" box popped, and things went back to normal.