Big Lipped Alligator Moment: Moment spent staring at the upside-down riverboat. Yes, they camp out in it, and yes the movie seems to imply the aliens are behind it, but... the fact that it is an upside down riverboat and is never explained and has no bearing on the plot - it wouldn't have made any difference to the story if they had stayed the night in an abandoned shack instead.
It falls into Fridge Brilliance territory once you figure out the real reason the aliens are there. Gold. And in the old west, a casino boat probably would have the largest concentration of gold outside of a mint. The reason it was upside-down in the desert was because the aliens didn't bother putting it back once they were done cleaning it out. It probably would have been more obvious if the group had bothered investigating the ship more than "It's weird, but let's head in there since it's raining and nasty out and we need somewhere to sleep."
So Okay, It's Average: General critical consensus seems to be that it was a decent movie, but considering that it had James Bond and Han Solo as cowboys fighting alien invaders, it should have been awesome.
They Changed It, Now It Sucks: It would take a full page to list all of the changes they made. Practically the only thing they didn't change was the main character's name.
The changes probably have a lot to do with the fact that the book didn't exist at the time the movie was sold to the studio, only a mockup of the cover did. They wrote it after the fact and production was already underway.