Also, some messages are in Henry's cell at the same time.
Henry - Henry is one of the more likely characters to be the one writing on the walls as many messages seem to be referring to him in the first person/would make sense to be him such as "I always fall", "I'm sorry buddy" and the tally marks in Chapter 1.They could also be begging for kindness or to stay out of their way, as on the staircase in Chapter 3, it says "Be Kind To People You Meet On The Way Up Because You're Going To Meet The Same People On The Way Down." Could it be that they just want kindness or something and they left that message for that reason? The Searchers/ Lost Ones - They and other characters write on the walls in order to be heard, but it could be theorized that some of them could have left the secret messages while writing around on the walls and somehow developed the Seeing Tool in order for others to see them.
Nobody knows who left the secret messages, although there could be some hidden theories of who's leaving them.