Hi @lukas.pavljuk,
how do you route your messages to the stream? If you use stream rules, can you check the order of your message processors?
I suspect it might have something to do with your issue, if you have the Pipeline Processor in front of the Message Filter Chain, your pipeline rules will never be triggered (messages are only routed to the stream after the pipeline handling is finished.) See Stream connections — Graylog 4.0.0 documentation for more background.
Cheers,
l0calhost