A few random thoughts/hypothesisings (sorry if they're obvious/obviously wrong/been discounted/just plain stupid) :
I reckon a few of the recent events could be fractures in time. (Bill&Ted 3 gets released this year, maybe they're to blame)
Orphan 55? The Doctor's seen Earth's future at numerous times so surely she'd remember if it ended up a radioactive, Dundonian wasteland. Unless there's been a fracture somewhere in the timeline and the Earth isn't
meant to be like that but the Doc somehow has her memory clouded as to what the timeline should look like.
Dr. Ruth (not the sex advice one) - somewhere the Doc's timeline fractured into two, resulting in a Ruth/Gat timeline where the Doc didn't develop sonic screwdrivers. Logical thing would be to go back through their memories and see where they diverge, maybe find the cause of the fracture (and fix it with some hyper-chrono-duct tape or something).
The Master's return - I'd imagine Missy would have a cloudy memory of her previous incarnation shooting her (the stronger the event, the stronger the memory). So it would be logical for her to do something to counter it, (knowing what and when it happens). A shield of some kind that absorbs most of the energy but leaves her mortally wounded but still capable of escaping and bodysnatching.
The Terrible Secret of Gallifrey : The Time Lords laid down the law. Made time nice and orderly. Only it's not. It's a chaotic mess with fractures and alternate timelines and continuity errors - and that was even before Gallifrey got into a time war/destroyed/hidden/found/destroyed again. The "fixed points" in time were installed by cowboy builders on a Friday afternoon. Rassilon was a backstabbing loony. Hoping to see the reappearance of Omega, the proper introduction of Abslom Daak and more refugee Time Lords emerging from hiding across the Universe (maybe they could found New Gallifrey somewhere, just down the road from
New Asgard...)