Are you saying that, for example, if you select the rectangle tool and click on the canvas to draw a rectangle, the move tool gets selected? (or similarly for other tools) This is of course not what should happen.
I don't know why this happens, but just like with Final Cut Pro, when the application misbehaves if often helps to delete its preferences (now called settings).
Start Motion and immediately press and hold Command and Option. A dialog comes up asking if you want to delete custom settings. Click Delete. Adjust the settings as needed, and see if the problem goes away.