It's almost an oxymoron to use the words "uniform" and "Mexican Army" together. The two main assigned uniforms consisted of cotton trousers and fatigue smock with a blue wool "overcoat," with white or buff crossbelts, for the regular infantry; and blue or gray wool coat and trousers with black crossbelts for the cazadores or rangers. The cavalry and lancers wore red, green, and blue according to some lost patterns or habits that I don't think can ever be reconstructed.
The epaulets, cuffs, and shako plumage tried to some extent to follow the regular color pattern for armies of the era, red, green, and yellow; according to the standard practice, the cazadores were considered the elite sharpshooters and some were equipped with the Baker rifle and sword bayonet. The evidence points to Santa Anna hoping to capture the fort before dawn with about 100 of these, many of whom slipped over the southwest angle before the surprise was blown.
Research done in the 1880s found that most regular Mexican troops at San Jacinto in April, 1836, were dressed in cotton fatigues rather than the common blue coat, and Santa Anna issued orders before the Alamo assault (March, 1836) that the soldiers were to leave their "overcoats and blankets" in camp. We don't know whether he meant the blue uniform coats or some additional coat worn over that, but this additional coat is not referred to as part of the ordinary soldier's kit.
The other problem is that many of the soldados were recently recruited or drafted and were poorly outfitted. Not many were given the full list of equipment or complete uniforms specified in the far capital. The prescribed uniform was a fiction drawn up for bureaucratic and funding purposes. The army was equipped with no medical supplies, regular reserve forces, or replacements for lost artillery, horses, or equipment.
It is likely that many of the men were wearing civilian clothing and sandals, straw hats, and didn't know how to maintain or properly use their weapons. It is true that Santa Anna ordered "raw recruits" to stay in camp, but it would have been difficult to identify and quarantine only those, especially in any 19th Century army with all of the shirkers. Besides that, the "reserves" were called up when they couldn't take the north wall-- 400 men, about half of them the elite zapadores (engineers). This means that the reserve column consisted of ill-shod and undisciplined rabble thrown in with upperclass educated troops in "big white hats" and wearing boots they didnt expect to have to mar in a doubletime march.
One of those engineers was an officer named de la Pena, and he held a grudge a long, long time.