Hi Sam @nodewax ,
What you are doing is a perfectly valid solution to the problem, but if you follow along correctly, the Separate by Selection, makes the Selected Faces into a new Object and they are no longer part of the ‘old’ Object (Crate). There shouldn’t be overlapping Geometry there.
My guess is, that you had overlapping Faces, before you Separated the Selection (maybe Insetting twice, without realizing it?).
If you want (recommended!), you can go back and try it again (maybe even do a M > Merge > By Distance, before P > Separate > By Selection).
