Alex being the one who hit Bethany That Night and it was her who Spencer saw. Spencer just assumed she was the one who did this because at this point it was the only reasonable explanation.
Alex being caught on NAT videos. That’s how they found out about her existence. That’s the reason why Melissa was acting so strange, why she was protecting Spencer from “before it even started” and why Ian and Garrett had to die.
It could have been what Maya knew.
Ian knowing about Alex and thinking it was actually her when he wanted to push Spencer off the Bell Tower.
Alex hiding in that creepy, haunted house and watching the girls.
Alex hiding in Jenna’s garage and getting hurt in the fire. Maybe not her face but her body so she still could impersonate Spencer.
Alex being the one we saw in the flashback from before Ali went missing that Spencer doesn’t remember.
Alex stealing the game from Mona because at this point she not only hated Spencer but all of them.
Mona asking Spencer to join A Team not only because Spencer was so smart. Mona noticed there were times when Spencer acted shady. She just didn’t know it was her twin.
Alex switching places with Spencer from the beginning.
Alex making Toby join the A Team and fake his death so she could mess up with Spencer’s head and send her to Radley.
All the British words or references during the show.
How A knew so many things about the girls and nobody never saw them.
Alex being Black Veil and that’s the reason why she needed to hide her face.
Alex dressing up as the masked man in the dollhouse and that’s why Spencer had a feeling she actually knew that person.
Seriously, the list could go on.
It’s all there. They could have used all of this and made it look like it was all planned even if it wasn’t. I’m not saying it would have tied up all the loose ends but it would make much more sense.