That's pretty normal for those boots. They're designed to be turned with the piston. Mine get a little hung up like that too. VERY CAREFULLY use something to push it back into the correct position and it'll be fine.
I like to clean and lube my brakes at least once a year and that involves pushing the piston down. To do that you need the tool to turn it. Yeah the boots get a little out of place every time. As I turn it in, the boot will twist. I just turn it back the opposite way a little to unfold it and turn in again.
And nice to see another Canuck lurking around here where abouts are you? Toronto area?