I'm midway through a replay of Chapter 1, here's a collection of things that amused me or otherwise hit differently the second time around. Spoiler warning: this is Chapter 1 content but there are some references to things that happen much later in the story.
There sure is a lot of foreshadowing of (or just joking nods to) being stuck in an infinite loop. All from before the first reset:
How many previous resets have ended with somebody blowing everyone up?
Press X to doubt
Aww, Ami wants to adopt Maya!
Pet the cat, Sensei
No really, PET THE CAT
This got dark knowing Maya's history
People keep saying that Maya's god is Wires, but we are clearly told who it is in Chapter 1
There is a very real chance that Sensei and Ayane are legally married
hmmmm....
Are you sure about that Sensei?
Sensei makes a trade offer
Ami+Rin scene waiting room
Sana casually sharing her mom's psychiatric history
Some cute foreshadowing
Previous Sensei and Yumi were totally boning
Miku knows more than she's letting on