When Chloe is riding on the train she is looking out a window. When you see the train from the distance there is no window in any train car.
When Rachel is in the bathroom getting ready with her friends, she clearly has her shoes on. She sees Chloe and walks out of the room, still with her shoes on. In the next scene when she walks in the room to fix Chloe's food, she has no shoes on, and only goes to put them on after Chloe has put the dog food in them.
The actors leave Los Angeles and arrive almost immediately in Sayulita, Nayarit, Mexico, which is obvious from the signs in the background in the small town. Not only with the drive from Los Angeles to the Mexican border be over 2 hours, even with decent traffic, it would be almost a day's drive to Sayulita.
When the girls first drive down to Mexico, they are in a BMW 328i convertible, which only has a single exhaust. In all of the other shots of the car, it's a 335i convertible, which has a dual exhaust.
When Chloe is looking out the door on the train-car at Delgado, the the train-car door is more closed then it is when Delgado jumps on the train. The door changes positions' during the whole scene.
The mountain lion scene would be incredibly unlikely in real life. For one, mountain lions are solitary animals and never hunt in groups (although the three that attacked Chloe and Delgado are possibly a mother with two full-grown cubs). Second, they only hunt at dawn or dusk and would never attack in a group out in the open in full sun during the middle of the day.
According to Papi's lovesick speech, Chloe has a raspberry colored nose. Apparently at least two "Chloes" were used. One with the raspberry nose, and one, most notably in the closing romantic scenes with Papi, with a black nose.
Puerto Vallarta doesn't have any railroads at all.
The Aztecs never colonized Chihuahua.
Tijuana doesn't have a train station. There's no way you could get to all the places they went at the short time they made going there.
When the dogs escape from the dog fights, you can clearly see that they go to Guadalajara's historic center, although this scene is supposedly in Mexico City.