It sounds like the usual confusion of war, doesn't it?

Santa Ana, unfortunately, did not regard the normal rules of war (don't kill your prisoners) as extending to the Texans, because he saw them as mere "piratas" (pirates). He didn't regard them as a legal army at all, therefore he showed them no mercy when prisoners were taken.

This kind of ruthless arrogance does not speak well for Santa Ana. After his defeat and capture at San Jacinto, Houston gave him his own life in return for Texan independence, and made sure that he signed a document to that effect.

This must have been rather disappointing to Houston's men, because they wanted to hang Santa Ana.