Before I start writing let me say this bug kind of makes logical sense, however it is annoying, and could be avoided with a bit of extra programming. Onwards
Normally -
If you complete all missions, you get your cool little daily present of 150 kobans.
Unless...
You complete all ur missions, but don't go back to the page before ur new missions arrive (much easier to do if u do ur "event" missions last) and click "Get Present", then you lose those kobans for good, although you did earn them within the time limit.
I think I have only missed out once, but still, ow.