Often when transcribing documents or records, the researcher thinks of "explaining" that needs to be done. That's fine--but just make it perfectly crystal clear where the actual document ends and the explanation or comments begin. One way to do this is to use brackets  and enclose your comments in those.
"I hereby leave until my son Johanna, my back forty acres after his mother dies [note: the document clearly says Johanna, but the reference is probably to son Johann.]"
You don't want people thinking your commentary is an actual part of the document, but you should always transcribe a document exactly as it is written--don't edit it while you type. That could lead to even more confusion.