At the cemetery the headstones for Jane's wife and daughter are reversed from the first time we saw them in "Cackle-Bladder Blood". In "Cackle-Bladder Blood", his wife's head stone is on the left and his daughter's is on the right. They are reversed in "Red Rover, Red Rover".
When Patrick Jane opens the box of Red John files on his bed at CBI, the first file is labeled "BRAGA, J P" and the third file is labeled "PANZER, J." Patrick removes the Braga file from the box and opens it. The close up shot of the file shows him reading the Panzer file. When Patrick Jane puts his hand back in the box, the Braga file is out and the Panzer file is still there.