We do document that our Python API uses reversed (Fortran) ordering, but I think it's hard for users to find this information. It would help if we could mention this in our Python error code #4014, which is ambiguous to the fact that we're not using cannonical ordering.
To reproduce:
1) Load any dataset with a 3D variable, such as ELEVATION.
2) Edit->Edit Python Program Defining New Variable
3) Create a 2D variable, call it E.
4) In the script editor: E = ELEVATION[:,:,0]
5) Click Test
Two errors come up.
1) Code: 4014 - Message: Shape of E array does not conform with BOUNDS
2) Output data error