If you'd asked Twilight which of her friends would break into her castle to commit an interdimensional crime, Applejack probably would've been pretty far down on the list, somewhere between Fluttershy and Princess Celestia. But between finding several unauthorized uses of the Mirror Portal, a sudden influx of unexplained funds to Sweet Apple Acres and a sharp increase of food-based magic incidents in the human world, it's hard to deny the obvious conclusion.
There's also the fact that Applejack isn't even trying to deny the obvious conclusion.
Warning: spoilers in the comments.
Literally last-minute prereading done by FloydienSlip.