Yes, it appears to be an editor bug. The meshes were not being unioned correctly to create a new polygon that encompasses all the meshes. I'm afraid the fix is only in 4.0.58-beta and later versions, as we're no longer doing 3.8 releases and 4.0 is nearly ready to go non-beta.
If you are exporting from the command line, you could use specify -u 4.0.58-beta
when packing your atlas.
FWIW, I don't think you'll see the bug in 3.8 if you use rectangular packing instead of polygon packing.