Levi Thomas would have had no reason that I can think of to identify himself using his old 1861 State Troops regimental designation, and since none of the other "3rd Arkansas" men served in that regiment, I can only believe that a clerical error was involved. It is just a coincidence, I believe, that the error made in his regiment affiliation happened to resemble his old State Troops affiliation.
By the way, as a side note, Gratiot's regiment was officially the 2nd Regiment, Infantry, Arkansas State Troops. However, the Northwest Division commander, Brig. Gen. N. B. Pearce, mustered it as the 3rd Regiment, Arkansas State Troops, so the Official Records generally use that designation. Just an interesting bit of trivia.