This stuff only happens if you are on a fast speed in geoscape, like 12hrs/second.
For example, manufacturing of plasma grenades is complete. So, as you have specified in the settings, the game pauses. You enter the base, and you can see the next item is already halfway manufactured!
The same happens when you go on a mission. If you are on a small speed while your Firebird approaches the location, you may enter it during daylight. But if you speed things up, the Firebird might enter the location at nighttime (later).
Absolutely reproducible.

It seems that the game does not pause right away after some event occurs. Like, while it opens up the confirmation dialog, the time keeps ticking.
I hope this is clear enough, feel free to ask any questions.