In the scene where Joe Kidd is approaching town after having joined up with Luis Chama, he sends one of Chama's men to ride into town first to test if the area is covered by gunmen. As he's riding into town you can see a vehicle driving across the frame in the distance.
Although the film takes place in the early 1900's the dress of many of the characters reflects a later time. The men's shirts button all the way down the front, several of the hats worn are of modern (1970s design) and the boots worn clearly don't match those of the period.
When the Harlan gang rides into the village, some of the riders pass in front of the church. The sun is very low in the sky, so low that the shadow from the cross, atop the front of the church, is being cast onto the wall of the church tower. In the following shot, Harlan tells Mingo to call the villagers into the street. Mingo rides back past the church, and the shadow is now completely gone from the tower, as the sun is considerably higher in the sky.
When Joe Kidd is kissing Elma, Harlan's girlfriend, they are interrupted by one of Harlan's henchmen (Gannon). Elma turns her head to the right to look at him. In the next shot her head is turned to the left as she looks back to Kidd.
The character of Joe Kidd says that he shot a buck mule deer "over south of Monero," and Mitchell says that's on the Jicarilla reservation. It isn't. South of what's left of Monero is not on the reservation; in fact, Monero is east of the reservation. In between Monero and Dulce (which is on the reservation) is a very small town, Lumberton. There is no way at all that Kidd could have been charged with hunting on reservation land if he were south of Monero.
When Joe Kidd and the towns people are imprisoned in the church, the padre tells Kidd that today is the Feast of St. James. The Feast of St. James occurs on July 25. Throughout the film, it clearly is on the shoulder of winter (fall or spring) with the characters wearing heavy coats and small patches of snow visible in the mountains around the desert.
The movie takes place in New Mexico, but saguaro cactus can be seen in the town (Sinola County) scenes. Saguaro cactus can only be found in Arizona, which is where those scenes were actually filmed (at Old Tucson).
When Harlan's gang returns to Sinola, Roy tells the desk clerk at the hotel that there are eleven of them. However, in the gunfight, we see the deaths of seven (including Harlan) and the surrender of two more. Two have disappeared.
When Joe Kidd gets the drop on Luis Chama near the rural village and orders Chama's ruthless, cutthroat gang to ride with them to the Sinola jail, the gang members miss innumerable opportunities en route to shoot Kidd in the back and set Chama free.
Just before Mingo is shot by Joe Kidd with the sniper rifle, Mingo's glove is shown already covered with blood, holding his own rifle. After he reacts to being shot in the chest, he presses the glove to his chest wound, then holds up his hand to reveal the blood.
In the early jail scene, after Joe Kidd throws the stew in Naco's face, he hits him with the empty pan. After the hit you can see the pan has no dent in it. Joe lowers the pan out of camera sight (you can hear it bump the table). When he raises it again, it has a large dent in the bottom. If you watch closely you can tell that he is changing pans out of sight of the camera.
When the shootout begins in the Mexican village, one of the bad guys is shot in a doorway, when he flies backwards into the room, the "brick" wall he lands against gives and then wobbles and shakes like rubber or card board.
The goof item below may give away important plot points.
When Joe Kidd shoots and kills Mingo on his sniper perch, he aims his weapon at Mingo's chest. This would have caused the bullet to drop and would have missed him by feet. To hit a distant target aim has to taken slightly above the target to compensate for the drop of the bullet.