In "Over My Dead Body," Jason says "I think my sister would want me here." We are made to assume he's talking about Ali but instead he is talking about Spencer since it was later revealed that he is her half-brother.
Remember Ali's alias, Vivian Darkbloom? Spencer notes that it's an anagram of the name Vladimir Nabokov, the author of the novel Lolita. (In which a character of the same name appears). Given The Reveal of "Now You See Me, Now You Don't", it makes perfect sense why she would choose that as her Secret Identity. She was using it to go see Ezra. It's the kind of reference that an expert on classic literature would appreciate.
In "UnmAsked", Mona says that she became A because Hanna was spending less time with her and more time with the other Liars, but the only time Hanna interacted with any of them immediately before the A scheme began was Spencer, when the two of them were talking in the mall. (It's explicitly stated that the four girls had been growing apart in the three years since Ali's death.) Assuming that Mona didn't make that up just to mess with the Liars, that would mean that she went off the deep end just because she saw Hanna having a three minute chat session with Spencer.
Later episodes imply that Hanna was good friends with Mona pre-Alison, and that joining the Liars' group broke them apart until Mona reached out to give them both the "queen bee" makeover. (The main clue being their "dream scrapbook" in season 7, which they supposedly made together in middle school. This is one of the very few times the show made a retcon that actually *fixed* several plotholes, like Mona's nonsensical claims that the girls "stole" Hanna from her.)
Ezra is not "A". He was just doing research to write a book about Alison's disappearance. Now, keep in mind that he had a ton of surveillance equipment. He knew that someone was hurting Aria and her friends, and he could have helped at any time. He could have used that equipment to help and catch the person, but he didn't. It also turns out that he knew Alison and had a brief fling with her before she disappeared. She was fourteen, and Ezra would have been a senior in college. Which also means that he knew how old Aria was from the beginning, manipulated her, and decided to pursue a relationship with her only to get answers. "Jerk" doesn't even begin to describe it.
In the books, in Unbelievable, Mona reveals that she was in the treehouse with Jenna and Toby when Alison (really Courtney) set off the firework that blinded Jenna and scarred Mona. A few books earlier, in Flawless, it’s revealed that Toby had been molesting Jenna and was doing so when Courtney set off the firework. Was Toby molesting or grooming Mona as well?
