I've had that happen while grinding 9hr Tsukaba in an FGT.
Not sure when it started happening, but when I turned the TV on with an hour to go, my Bob's were a dozen laps behind...WTF.
I had to command "cancel pitstop" for the rest of the race. Hasn't happened since.
I ran Bob for the first 12 hours of Lemans24Hr, went to bed, switched on for the last 4 hours and nearly every opponent was pitting every one or two laps. Don't know why.