The way we see it is... after two sieges and a bloody battle, many buildings in the Alamo mission compound were damaged, burnt or pockmarked by heavy cannonade. Before he marched east in pursuit of Houston’s small army, Santa Anna assigned Colonel Juan José Andrade and his troops the task of repairing and occupying the Alamo. The Mexican Army maintained control of San Antonio until May 1836. That month the soldiers of the Mexican garrison received orders to demolish the Alamo before they withdrew. They knocked down some of the outer walls of the compound, including the log wall known as Crockett's Palisade, so it could not be easily refortified by the Texians.
Many of the wounded Mexican soldiers had been housed in San Antonio following the battle. Several Texian doctors captured with Fannin's command were sent to San Antonio to help tend Santa Anna's wounded, who were then evacuated in May and June during the withdrawal.
Texian forces under Captain Juan N. Seguín entered San Antonio on June 4, 1836. Seguín reported that 18 Mexican soldiers, under the command of Lieutenant Don Francisco Castañada, were present when he entered the town.
Relations between the two groups were peaceful and Castañada and his men withdrew two days later.
The Texians evacuated the town several weeks later once it became clear that the new government was unable to send reinforcements.