Plot hole: The only reason Kate is brought onto Matt's team is to give the CIA legal authority to operate on US soil. Given that he already has DEA agents and US Marshals on the team, all of whom seem to be fully aware of what he is doing and have no problem with it, this doesn't make a great deal of sense. Her idealism makes her a poor choice for the sort of operations the team is doing, and there are already domestic US agents available.
Plot hole: Nicky steals the EXR formula from Garriga's "server" by hacking it remotely within 48 hours. That's impossible. Garriga wouldn't carry his servers to race tracks. He needs only the fuel with which to race, not its formula. That means Nicky was left with penetrating air-gapped R&D servers inside Garriga's factory. This task is worth an entire film unto itself. It can't be done in 48 hours.
Plot hole: Echelon controlled satellites hit targets on Earth with pinpoint accuracy. A lot of them involve creating storms to ravage an objective. One of them is started over 18 hours away from the target (how they know is another mystery), but this is what gives the characters time and allows the movie plot to continue to the end to defeat Echelon.