I have come across an issue with random crashes happening in black mesa for Linux users, it seems that the openGL drivers and the mesa 3D graphics library are out of date which steam uses by default in their runtime folder.

to fix just run each command in terminal to make sure you have the latest libraries (you will need APT installed, I am new to Linux so if you want to add the equivalent for each package manager just list in the comments).

sudo apt-add-repository ppa:oibaf/graphics-drivers
sudo apt-get update
sudo apt-get dist-upgrade

This fix was based on an Ubuntu 18.04 distro, good luck! :)