I had a support request regarding this issue. The support team confirmed the issue and answered that the problem will most likely be remedied in 2022.1, but I just want to post here as well to inform the community in case anyone has similar issues.
I use the Docker toolchain in CLion for developing ROS-code. The ROS dependencies requires me to source a setup script in the entrypoint of the toolchain image. This worked fine in 2021.3, but was broken in 2021.3.1. I figured out that the entrypoint of the image was completely bypassed after that update. I suspect CPP-27316 is the culprit.
I think it's worrying that the interface is changed so significantly without proper documentation. Thankfully I believe JetBrains will sort the issue out by adding options for the Docker toolchain command (CPP-27348).
I temporarily fixed this by rolling back to 2021.3 https://www.jetbrains.com/clion/download/other.html