The crumpled Note from Frank only appears if you give Frank's note to Bill in the garage during High School Escape. Bill reads it, crushes it and tosses it on the floor; pick it back up for a separate artifact.
Joel hesitantly hands it over. Bill reads it, curses Frank out loud and throws it away, clearly hurt by what his partner wrote.
Pick up the first note before talking to Bill, otherwise there is nothing to give him and this one never spawns.
Bill's Map
Bill's Map is Bill's hand-annotated map of Lincoln, on a table with an engine near the door you come in through at his safehouse, right after you meet him.
Bombs Note
The Bombs Note is on a table to the left in the side room off the nave of Bill's church. Go into the room on the right, the one Bill makes clear is not the confessional.
Boy's Diary
The Boy's Diary is on the windowsill of a child's bedroom painted with stripes and cars, upstairs in the second house with the dry pool in the new territory beyond the church graveyard.
Fences Note
The Fences Note is another of Bill's reminders, on the table in the back room of his safehouse near the pipe he handcuffs Ellie to.