The game crashed once after unocking the secret creature. I did notice before that, the game was becoming more and more unstable, more and more frame drops until a reload. Not sure if its unoptimized or a windows game in Linux issue.

I assume this isn't truly related to running it in Linux, however, it might be less stable than in Windows and more prone to crashing. On the current version, there is bug related to the unlockable creature. If the game crashes after turning in the final symbol and getting the achievement, but I assume before the next save after getting the unlock message for the creature, then when you load up the game again, your save might be permanently locked out of the creature spawning in.