With Jane having to battle some mean moms during "Chapter 57," The CW show was really loving on Mean Girls and it came full circle when Scott's burn book was discovered on Jane the Virgin. While the series did not show the inner contents of the book yet, it does not look good for Petra that she had been hiding the dead man's diary. Considering how Petra might be Scott's number one target in his Mean Girls-inspired book, the police are most certainly going to want to investigate her.
As the movie Mean Girls showed, a burn book is a place for you to write really nasty things about people — so I guess I shouldn't be surprised that the jerk Scott had one. And Rafael was acting shady in "Chapter 56" because he was having his prison friend Elvis steal this book from Petra. Rafael's intentions on why he was snatching the book haven't been made clear, although there is a possibility that Scott isn't really dead and Rafael has been working with him. However, that won't help Petra right now since after Rafael broke up with his girlfriend Abbey, his angry ex blamed it on Petra and sent the burn book to Dennis over at the Miami police department. And knowing that Petra had a bad relationship with Scott and that Petra was hiding the book just might make the police think she murdered him.
Since the series hasn't been bringing up Petra's identical twin sister Anezka since the show jumped in time, I'm sure that she has something to do with the mystery surrounding Scott. Rather than thinking that Petra killed Scott (wouldn't that be too obvious?), Petra's secrecy could be because she's protecting her sister. If Anezka and Scott's marriage went bad, then Anezka and Petra would certainly take up a lot of space in Scott's burn book. So while Petra might not be guilty of murder, I'm not so sure about Anezka — or their criminal mother.
Another factor that's going to put Petra in even more trouble is that she confessed to Chuck that she had moved Scott's body onto his hotel's property. She's not stupid enough to confess to moving the dead body of the man she murdered, so while I think that's another indication of how she didn't kill Scott, Chuck could still tell the police about Petra moving Scott. That, along with the burn book, could lead to Petra being arrested since tampering with a potential crime scene is bad enough. So somehow, even in death, Scott has continued to torment Petra — and this time, he might succeed in really bringing her down.