I've had this happen to me twice, but I noticed the details a bit better this time.
I kicked the ball with a player with the kick skill. Of the two circles that came up, one of them was out of bounds and the other one was in bounds. I clicked on the in bounds circle and then the ball immediately was kicked out of bounds.
I went back to watch the replay, and it was a bit strange. On my first kickoff of the match (turn 1) the replay clearly showed two circles on the pitch, and my selection of one of them. The ball went to the selected square.
On my second kickoff of the match (turn 5, the kick in question), the two circles show up again. But the replay did not show any square chosen and the ball was kicked out of bounds. I know I clicked the pitch on the second kickoff, but it is not shown in the replay. The time that the counter showed should not have resulted in a time out as I clicked the field immediately, but the result sure seems like the game thinks I timed out and didn't pick a square.
Match was this afternoon, Kislev Test Hoppers vs an Ogre team if you would like to see the replay. Only match Test Hoppers played on this day (8/29/2017).
The other time I remember this happening was also one where one circle was off the pitch and the other circle on the pitch.