Yup... happens to me all the time. To avoid the sometimes massive hold ups in the pits I usually pit early or late in my window. Pitting early, that is to say before my race engineer tells me to, results in him asking me to pit on every lap thereafter till the end of the race. Annoying, but not a game stopper ;-) Even asking for a pitstop before going in does not remedy this bug.
Playing xbox360 version.
-Greg