The document with the crucial slip of the pen as corrected by Tsar Paul I is clearly not the same as the one written by the army scribe in the previous scene. In the first version, the second (mistaken) letter K is clearly larger than the first. In the version corrected by the Tsar, they are the same size. (Though the subtitles have the Tsar capitalizing the second K, what he is actually doing is adding a letter between the two two Ks - the Russian "hard sign" required at the end of many words in the pre-revolutionary spelling system. The effect is the same: to create a fictional Lieutenant Kizhe.)
In a scene after 'Colonel Kizhe' returns from Siberia, in one shot his escort is standing with a curtain on his left and in the next he holds the curtain in his right hand obscuring the left side of his body.