Plot hole: When being arrested after the car chase, Hunt and Grace are told to put on the handcuffs. They have their hands up, and neither is holding the cuffs. Then, fired upon, suddenly they are cuffed to each other. Even if explained as a sleight of hand out of shot, from a plot point of view it makes no sense for either of them to cuff themselves to the other at this point. Hunt is trying to save Grace, which makes it harder to do so, and Grace is trying to escape from him, not anchor herself.
Plot hole: Benji puts his car into automatic mode, which operates partly through satnav. Surely, this would be monitored by The Entity, who has predicted every other action up to that point. The same car is used at the end of the film, but if The Entity hasn't noticed it by then, it's not as powerful as they think it is.
Answer: While it looks like a normal Fiat 500, this is a specialised IMF car, as evidenced by the controls inside and its ludicrously high speed. It being electric is in line with that.