When Jake is looking up through the hole in the roof of his house, there are two crossed boards held together by a screw with a recessed head. The square or Phillips headed screws were not invented until the early 1900s.
When Jake is riding towards his house, the scene is a long shot but it can be seen very obviously that the bracelet is missing from his arm. In the following shot the bracelet is suddenly back on his arm.
After the first Alien attack at roughly 45:20 into the movie when Jake Lonergan rides after the Aliens on his own, his bracelet is seen missing for a few seconds until a close shot where the bracelet is back.
The three cowboys Lonergan meets after first waking up appear very dirty and sweaty, and all of their equipment is old and used. The cowboy hat he later takes from one of them is obviously new, as it doesn't appear dirty and doesn't have a sweat salt stain where it would rest on one's head.
The Apache chief needs a translator to communicate with the cowboys, except in the scene where Ella tells them all who she is. In this scene, there are a few times when the Apaches appear to understand English.
The morning after the first alien attack, the posse follows the trail left by the alien which, according to the dialog, headed North. However, the early morning shadows cast by the sun on the the riders and their horses are on their right, which indicates that they're riding Southward.
When Jake encounters his old gang, he punches in the mouth the first guy that comes close and who had recognize him. He has blood on his finger in the next shot. A few shots later the blood vanishes and after several shots it reappears.
When meeting up with Jake's old gang in the valley, they are told to put their hands in the air. In one of the shots Ella is seen getting off her horse. In the next shot, immediately after the previous, she is standing beside her horse, but there is no way she could have gotten off her horse so quickly.
When Woodrow and the rest of the men on the trail of the aliens arrive on horseback at the upturned boat, it is raining heavily. However, no rainwater appears to be dripping off the brims of the men's hats.
After the first alien attack it is stated that they will leave at first light, but the next morning from the length of the shadows on the ground it can be seen that the sun is up and it is well into the morning.
The goof items below may give away important plot points.
When Jake Lonergan and Colonel Woodrow Dolarhyde are escaping the alien stronghold, Jake is hit by a blast of dust as they emerge from the cave opening. In this shot, Jake is clearly covered by dust, however in the next shot, he is again clean.
Although Ella explicitly states that the aliens are blinded by bright light and avoid it, they later appear to have no compunctions about fighting in full daylight nor do they appear to be inconvenienced in any way by it.