I think this is a bug. I started building the assembly step-by-step until the hole appeared. I found that the hole comes when I insert a block.
In the attached,I have a the solid and the block. The solid has the hole in it. If you cut the block, the hole goes away. If you paste it back, the hole reappears, even though the two are not joined.
Hi Jim - it looks like the edges have been forced closed in some places - like right where the ‘hole’ is. If you Explode, the RebuildEdges (defaults) and then Join, you’ll see there are nakeds - it does not join up nicely.
Ah, wait, I see your tolerances are very small… hang on a bit.
It’s fine you can just fine tune the document mesh settings so that the ‘Maximum distance edge to surface’ is .01, that should clean it up.