Hey there folks,
Taking a look at the question, a quick search brought up the possibility of the 11th AL's flag being one that was captured, but for sure there was at least one if not more taken after the fighting was over. Here is an excerpt from a book called Crossroads of Freedom: Antietam by the famous James McPherson,
"An enlisted man in this [New York] regiment who had captured a Confederate battle flag in the sunken road wrote in his diary on September 19:
'[sic]Today I was given detaile to burry the Dead Rebels, just where I captured the flag at 2:00 PM of the 17th. 12 lengths of fence being counted off for my station &
in 10 rods [55 yards] we have piled and burried 264... & 4 details has been obliged to do likewise, it was a Sight I never want to encounter again.'"
Similarly, the 44th AL had their flag captured by a 2nd Lt. Theodore W. Grieg, Co. C, of the 61st New York Volunteer Infantry. Link here
Again, the Alabamans had no luck when those of the 13th Infantry also lost their flag, this time to Private John Murphy of the 5th Ohio Infantry. Link here
So with the amount of dead piled up from all the regiments, I can see several of the other states' regiments present would have probably lost theirs as well, but no links just yet to show for it.