In my opinion I believe you were correct the first time thinking it was a mistake.

The following may give some insight as to where the mistake may have occurred.

Anytime a large amount of prisoners were taken from various units mistakes are bound to happen. The same was true at Helena, Arkansas on July 4, 1863. In a perfect world the prisoners would have given their name and unit and the Provost Marshal would have tried to extract additional information from them. Mistakes may have occurred in numerous ways. False information from the prisoners, Union soldiers interpreting or spelling the wrong names and units etc. General Ainsworth and his staff started making the Confederate CMSR's in 1903 and perhaps once in a blue moon the clerks have also made some errors.

In this case the mistake was made during the war and not after. The clerk for General Ainsworth who complied these records was Mr. Maynard. Mr. Maynard caught some of the mistakes correctly but missed a few too. One of the ones he missed was Levi Thomas. And he missed it in the respect he did not list an alternative named unit with the 35th Arkansas as he had done with many others.

Looking back at the copies of the prisoners of war at Helena I see at least 10 soldiers who were with the 35th Arkansas who were listed as being with the 3rd Regiment, Arkansas Infantry. We know the 3rd Regiment, Arkansas Infantry was at Gettysburg and could not have been at Helena, Arkansas on July 4, 1863.

It is interesting to note that soldiers such as Philander L. Snow and Jesse B. Jackson and James H. McConnell were all prisoners taken at Helena along with Levi Thomas and with the 35th Arkansas which was also known as other units mentioned in prior messages. However these soldiers and many others were also listed as being with the 3rd Arkansas after their capture. In some cases they were listed as being with both the 35th Arkansas and the 3rd Arkansas and in other cases with the King's Regiment and the 3rd Arkansas and all with Mr. Maynard's name on them.

In my opinion the mistake happened either at Helena, Arkansas or at Alton, Illinois by a Union clerk.