When transcribing any document, make no changes–even if something looks blatantly incorrect.
Annotations or comments about the incorrect part of the document should be made in a way that clearly indicates they are not a part of the actual document itself. My own personal preference (which we utilize in Casefile Clues, is to start a transcription with [begin transcription] and to end it with [end transcription]. Between those markers only the transcription of the document is included.
Comments about the accuracy are made outside those brackets. [sic] is used within the transcription for the occasional word spelled incorrectly or other blatant error. That notation is simply used to indicate that something was copied exactly as written and that it was not a transcription error introduced into the document when I was transcribing it.
Don’t fix the document when transcribing it. What you think is wrong may end up being correct.