So I start drawing a square, drag it open, and click on the first dimension. I type in the correct first dimension and it does what it should. I type in the second dimension and it becomes a triangle and moves in the opposite direction.
Have you tried Exiting Shapr3D completely, and then Restating it and attempting the process agin?
Alternatively Shut Down the iPad, wait 20 seconds before Restarting it and then attempting the process.
I did get it to work eventually. Just curious how this happens to begin with.
I find there are often ‘glitches’ when the iPad has been used for a long period without either of the things I mentioned being done.
Usually after every session S3D is properly Exited as a matter of course. I mainly use this iPad for S3D.
Glad to learn you are happy with the new iPad, let us hope for more good things to come in the shape of iPadOS 
It happened because in the current implementation rectangles are just four lines and not rectangles. This will change in the future.
Not entirely sure I follow.