Yeah there are some, none I don't think are required. Jacobs missions require you to get to a certain location by a certain in-game time. There is no meter or anything that I have seen. You have to open your phone and look at the clock.
As log as they are not missions required to complete the game then I see no problem,If there are some timed missions that need to be completed then I sure hope CH can put a stop timer or reset timer option in a trainer.