Kane shoots Joseph in the right shoulder, after Kane is killed by the steam, we see a somewhat closeup of Joseph and the bullet hole is now on his left shoulder, it later goes back to his right shoulder.
When Joseph and Jude arrive at the mine, they are each riding a quad, which they park outside the gates. When Kane and Jude emerge from the mine, in the background you see only one quad.
Grant states that there have been a thousand years of European intermarriage with the Mayans. Europeans discovered the Mayans in the early Sixteenth century, so there has only have been at the very most five hundred years for interbreeding to occur.
The "Twelve Days of Christmas" is an English carol derived from an older carol from northern France. There is no evidence of a connection to the Spanish, and certainly no connection to the Mayans.