Factual error: The Skycrane helicopters have a max takeoff weight of 42,000 lbs. With them weighing in at 19,200 lbs, that leaves 22,800 lbs that they could lift. Even small carracks, the ships, weigh around 180,000 lbs.
Factual error: Chloe and Nathan use a GPS tracker in their phone while Sully is above them searching for key holes. They're both able to stay together due to this. The problem is Chloe and Nate are underground. GPS uses satellites and they wouldn't work underground.
Factual error: Nate and the other chick find four amphoras full of salt inside an ancient Roman storage room underneath Barcelona's streets. When they burst, the salt is released and spilt everywhere. Salt is a very hygroscopic mineral. It is impossible for that salt stored underneath the city's streets in a non-sealed container to not be one giant block of wet, melted solid after 500 years of humidity. It happens to kitchen salt if not stored in a dry place, let alone salt from the 16th century.
Factual error: When Jo kills Santiago by slitting his throat, there is only a trickle of blood. He should be covered in it. This was probably done to keep the PG-13 rating.
Factual error: When they were in the underground chamber and it was filling up with water. Nate is still talking to Sully through his phone app, despite his phone being in his pocket which would make the call so muffled as to be inaudible.
Suggested correction: Nate was talking through the device in his ear, the issue with the phone is it breaking since it was submerged in water. The Bluetooth piece in Nate's ear is how he was communicating, not the Phone GPS App.
Factual error: When Nathan and Chloe are freefalling from the plane, they're able to communicate with each other. This is physically impossible. They're probably falling at a speed of 120 mph a second, which would literally suck the air from your lungs if you tried talking at the altitude they fell out of the plane from.