As I understand it, yes, a 3 point lift piston can come out of the cylinder (inside under the seat) and get cocked at an angle and won’t go back in.
Do you have a parts book that shows the parts for the 3 point? If not, go to one of the dealers such as Circle G or Affordable and look up the 3 point piston. That will show you how things go together.
If you drain the fluid and take the back cover off, you may be able to see what is going on inside. You might get lucky and just have to lift up on the arms enough to get things back in place.