Hi,
I got the same problem, last month, only 3 days after I bought the car from the Skoda dealer (it was a 13K miles car owned by one of the bosses of the VW dealership).
After the engine light had been cleared, they told me that this warning came from the secondary cooling pump that had already been replaced after a Skoda service campaign in end 2015.
Till now, no more problems with it (sometimes (and fortunately), I can hear the pump doing his job ,after an intensive run, and when I leave the car).
So no, this is not an isolated incident, but our common point is 2015 !! (mine is from july 2015).
