Which makes 0 fucking sense and made me rage quit the game.
Please read how to report bugs: https://ludeon.com/forums/index.php?topic=513.0 (https://ludeon.com/forums/index.php?topic=513.0)
Mortars vs. mountains is an old topic, and has been studied several times.
https://ludeon.com/forums/index.php?topic=46131 (https://ludeon.com/forums/index.php?topic=46131)
https://ludeon.com/forums/index.php?topic=51084 (https://ludeon.com/forums/index.php?topic=51084)
It is almost certainly a section of thin roof inside the mountain.
A save is required, randomly bombarding mountain bases again is a waste of time.
If you can provide an unmodded save that has a flying mortar shell that is going to punch through thick roof, amazing!
If not, well, you're not the first to miss a section of thin roof.
As Ark mentioned, this probably is the game working as intended, some parts of the mountains are not thick roofed, the thick roofed parts are immune. Without a save, I am going to assume that was the case.