When Blondie and Tuco are captured as Confederacy soldiers, Angel Eyes is a Sergeant in the Union army.
Is there any explanation for this or is it just assumed that he stole the papers and the uniform from a dead Union sergeant?
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You can find in the IMDb FAQ an answer to the question
Was Angel Eyes really a Union officer when Blondie and Tuco are captured?
No. He was only disguised as one to get closer to the gold. It's possible he murdered the real Union officer and stole his identity. In the film novelization by Joe Millard, after the battle of Glorietta Pass, he finds the body of "Sergeant Allen Crane", assigned "to adjutant duty at [Battleville] Prison Camp", and steals the man's orders and uniform.