Plot hole: The nuclear codes are stolen and the Russian guy holding them was let go by Dom. He would contact his government to let them know and the codes changed. Cypher would also know this so her plan is flawed.
Plot hole: Anything conducting electricity within the blast radius of the EMP, and not in a Faraday cage, would have been permanently fried. Since the whole base was within the radius (needed to take out the gate) including Dom's car and the Submarine, Cypher's plan was flawed from the beginning.
Plot hole: Dom arrives in New York at the same time as Hobbs and his team. Dom meets up with Shaw's mum and then proceeds to steal the nuclear codes. Meanwhile at the same time, Hobbs and the team arrive at their secret hideout and start preparing the cars. The time frame isn't the same - Hobbs and co. simply haven't got the time.