Pinkie Pie's abilities have confused ponies for as long as she's been around. Her very existence is an oddity, and maybe there's a reason for that after all.
Equestria Girls. Twilight has a bad experience with a rude woman at the store and blows up at her. Pinkie is upset by this, but not for the reason that Twilight thinks. Thr3shot: Hurt/Comfort with a bit of angst, followed by fluffy platonic cuddling.
Rainbow Dash keeps forcing everyone to read a comic that isn't funny. Twilight tries to find out why and Pinkie Pie is, as usual, completely unhelpful in a deeply unpleasant way.
Twilight notices Pinkie Pie acts strangely whenever Maud is around or even when other ponies mention her. When she confronts Pinkie about it, the earth pony's reaction is far stranger than she ever expected.
Twilight is haunted by nightmares of actions done long ago. Unable to sleep, she seeks comfort where it all began. Pinkie suffers anxiety attacks and doubts if she really is the Pony she thinks she is - her thoughts driving her to where it all began.