Kronk is shown killing the same three Indians twice.
During the Indian attack, the Chief's son falls off his horse (several times). He is shown on the ground wearing no shirt and when the other Indians pick him up he's wearing a buckskin shirt.
In the lead-up to final gun fight between Sam Hollis (Dean Martin) and Don Andrea Baldasar (Alain Delon), as Sam Hollis is walking to "his" end of town, Sam's shadow falls to the right but when Sam turns to face Don Andrea, Sam's shadow now falls to the left. Several hours would have had to elapse for this to occur.
Rodney leads the 6th Cavalry, but the 6th Cavalry wasn't established until 1861, 16 years after the film is set.
The Comanches are riding horses with obvious saddles under horse blankets.