that could cause mis-identification.
easiest example i could come up with is mp3 file with ID3v2 tags. unlike ID3v1, which is stored at the end, ID3v2 is stored at the begining. becuase ID3v2 is so "versatile"
there is no defined size for such tags...they can have just track info, or lyrics to a song, or even album cover embeded into mp3 file.
if you don't read enough info you could transfer bin file as ascii. but what is enough?
Almost user, untill there is better solution you could transfer everything as bin and then run program that will convert "bad" txt files transfered as bin to correct mode.