Sitood sent me his map and I managed to find the cause of the error.
tl;dr It was a displacement creating somehow weird geometry and deleting the displacement fixed the error.
If you get comparable errors in the future and you don't know how to find the cause: I just used the cordon tool, put it around the spawn room and compiled the map with the lowest compiling settings (Normal BSP, fast VIS, no RAD. Takes like 1 second). The error didn't show up so I increased the range of the cordon box rather generously and compiled again. I did that like 3 times until the error started showing up. Then I decreased the range again by smaller steps until the error disappeared. It's rather easy to guess which room had the faulty geometry by that way. I just removed the only parts that were complex geometry in that area, which were the displacement walls and that fixed it.