There are more, but here are some clues to most of them.
1) Day 9, Paige/culprit talk.
2) Leet speak.
3) Day 13, Paige talk. Pre-laptop
4) There are 4 hidden numbers in the Escape Room, unrelated to the gate code
5) Bonus color puzzle after completing Escape Room
6) Pervert's Password - Mentioned by Paige on Day 15
7) Flashback on Day 15, Paige is weird
8) Group chat on Day 16 - Your Master
9) Completing all the Paige Puzzles and then getting the bonus scene and choosing a certain choice at the end
10) Day 17, Mess Hall. There is a 4 digit code on display throughout
11 & 12) Day 19 pt 1, Jendayi/Aoi memory recalls
13) Day 19 pt 2, end of night talk with Ishani