That's what's written in trainer troubleshooting: "I have tried running the trainer, running the game, alt-tabbing to trainer and pressing F1 to activate and then alt-tabbing back to game to use options."
I always start the trainer as administrator. But when I press F1 the game crashes. Then I try to restart the trainer and the game. After that I alt-tab to the trainer and then press F1. But the game crashes anyway.
I have the game version 1.06.329 but there no trainer available for this version. Maybe that's the reason. Also I have several DLC's purchased.
There is a new trainer for this game, for version 1.06.329.
I'm guessing you have the UPlay version. The 06.11.2016 version crashed my games too. I had been using the 1.06.328 version successfully, until the Windows Anniversary update broke it.
Try the new 1.06.329 version. I've been using it today with Watch Dogs Complete Edition 1.06.329 with no problems.