What am I doing wrong with these wooden frames?

OK so I'm trying to build a rabbit hutch but I have two problems. Firstly one side of the frame which is made with 3x2 sticks out in one corner. I've tried aligning it with no success. I even tried laying it on a floor I know to be perfectly flat. One corner always sticks up and I can't figure out how to solve the problem. I thought perhaps one of the pieces of wood was bent but this is not the case. What am I doing wrong here?

Also on the small door which is made from 2x1 wood. I screw the top and bottom pieces to the sides which are all the same length. This in my mind suggests that a square should be achieved. However this is not the case. When I hold up my finished product in front of me I see that one corner of the frame is higher than the other corner, and as a result the bottom corner is higher than the other corner too. All the wood is straight so I don't understand why it is taking this shape.

Please, if anybody can help me with these problems please respond. Usually if I don't have the skill to do something I can relax and practice to get better. However this not knowing WHY I am getting it wrong is doing my head in. Once I know HOW I can practice.

Thanks for your time, Dave.