Yes, the Texans at the Alamo had received a direct order from Houston clearly instructing them to abandon the mission and join the main Texas forces, and they deliberately disobeyed it.
So what? The defenders of the Alamo died for the cause of freeing Texas from Mexico. Besides, there's no way of knowing at what point the defenders actually got the message from Sam Houston. It's not like they had radios, or cell phones in those days.
An order from Sam Houston to evacuate was not mentioned anywhere in the movie nor on any historical markers at the Alamo historical site. The letter from the fort commander asking for help was mentioned as one of two denied requests that he made for troops from a fort about two days journey away.
It also mentioned that all defenders were killed during the battle.
300 or so men were captured at a later battle and 10% were subsequently executed at the request of Santa Ana (chosen by drawing black beans or white beans from a hat)- against the pleadings of his commanders to not execute men who had surrendered. No mention was made of 6 defenders being executed.