Hi Charlie, that's probably a bug in something like surface combining but it's pretty hard to figure out where the bug is looking at just the aftermath.

The side walls for that hole has a broken surface where it's only got half the surface that should be there, it looks like this:



It's hard to select broken faces like this, sometimes window select can work but also if you select the top and bottom faces and use Edit > Separate it will get shook out, then select the other pieces and use Edit > Join to glue them back together then you can invert the selection to get that bad piece selected and delete it.

Was this model only built using MoI v4 or did you use MoI v3 for some of it? It's kind of similar to a cylinder combining bug that was fixed in v4 but maybe there is another type of combination that is still buggy.

- Michael