Versions

• Minecraft version 1.16.5
• Forge version 36.0.39
• Mod version 1.16.5-1.1.2

I have setup as shown on screenshots:
I have incomping flow of Mystical Agriculture Essences and Seeds going into buffer barrel with single pipez output (advanced pipe upgrade). From that output Essences are configured to go to Crafter, and Seeds to Seeds Reprocessor.
I have another advanced pipez pulling Essences produced by Seeds Reprocessor into Crafter
Problem is that some Essences go to input of Seeds Reprocessor, despite only Crafter is whitelisted for Essences.
Blacklisting Essences from going to Seeds Reprocessor does not help.

Screenshots (Optional)
Screenshots of the issue:

It does not happen if I blacklist Essences from Seeds Reprocessor output go back to itself, so they just take shortest path instead of following existing whitelisted path to crafter. Still its not logical that whitelist does not have priority leaving place to situation like that. In case that there would be more destinations, routing like this make logistics impossible with only whitelists and blacklisting manually all possible destinations is extremely time consuming.

Your seed reprocessor still allows iron essence to be inserted. You either need a blacklist for it on all other destinations or make a whitelist for other items on all other destinations.

It does not happen if I blacklist Essences from Seeds Reprocessor output go back to itself, so they just take shortest path instead of following existing whitelisted path to crafter. Still its not logical that whitelist does not have priority leaving place to situation like that. In case that there would be more destinations, routing like this make logistics impossible with only whitelists and blacklisting manually all possible destinations is extremely time consuming.

Whitelists don't mean priority.
If you create a filter entry with a destination, it is only applied to that exact route - completely independent to all other connections.
For basic tasks this seems a bit counter intuitive, but for more complicated setups, it is necessary.

Thank you for explanations. I fixed my setup using blacklists only. Should the issue be closed then?

Yeah I'm gonna close it.