Typical that the last thing I need to do for 100% bugs on me.
I think it's the northernmost challenge tomb where the skinny posh girl floats the bomb ball down the stream through the gates. I think the tomb entrance is still glowing like it's incomplete but I've done it ie I collected the upgrade and the gun. He only challenge tomb to have 2 final chambers guarantee this is what caused the glitch.

I remember this much
I did it solo.
I bombed the bottom right room first then exited before bombing the top left one.
I may have taken a shortcut with escorting the bomb because of my leet skills.

Tried deleting and reinstalling. Nothing.

Any thoughts crystal D?