When Carol writes her letter it reads "John, have gone to space ship. Carol." But when John receives the letter it reads "John, have gone up to space ship. Carol." The location of the ink smudge in the left-hand margin also moves.
Susan smudges the letter to prove that the ink is still wet, but the smudge was visible before Susan and John had received the letter.
The Doctor reads the visible letters on the feral human's shoulder flash as "I-N-N-E-R" when they clearly read "INEER", the final letters of Engineer.