I'm a hardcore mountain enthusiast; every game I've played for the past 900 hours has been in the mountains. One thing I noticed is that once every few sieges (2-3) that attack me, one ends up lobbing at least one mortar shell directly through an overhead mountain tile. I figured that this would've been reported ages ago as I've had it happening since B18, but almost all reports are responded with "Can't replicate" or "Probably hit a thin mountain tile." I'm also a vanilla only player, so I'm positive it doesn't have anything to do with mods either.
Replicating the bug is honestly probably the biggest issue because I have absolutely no idea what triggers it. Typically the shell that gets inside is an incendiary and typically it happens near a smooth wall. All I can recommend is to play on a large size map, dig out a massive room, smooth some walls and wait to see if a siege hits your colonists inside the mountain.
Here's a screenshot of my most recent hit to prove I'm not crying wolf
Can you upload a savegame where this just happened, preferrably with the debris still in place so we can see the exact location where it hit?
Even better would be a savegame where the mortar is about to hit (save before every shot).
The most likely explanation I can see is that there are a handful of normal roof tiles among the overhead mountain. You could try to find them with careful mousing over perhaps. The savegame would also be good to dig into!