Modpack: New Game
Modpack Version: 86.0.0
Mod Version: 1.0.1.985
Minecraft Version: 1.20.1

I have a weird bug using Sophisticated Storage Controllers on my server. I'm using a storage controller with some link blocks to automate sorting. The controller has a chest with hopper upgrade on it and I activated "Match Stroage Contents" Filter. However for some reason when I put Copper Ore there it doesnt get sorted. Every other item, even if its going to the same chest, is working (at least the ones I tested for now).

Ah my bad now it works, thank you. Didn't think of that as just copper ore wasn't working for some reason.

From your description it sounds like the the input chest sits directly on top of controller which makes connect to the controller multiblock and become of it and as such it is one of the storages that controller inserts into. So what is likely happening is that the chest actually inserts the copper ore into the controller then controller figures out that the same chest is the first one it should be inserting copper ore into and just inserts it right back.

You would want to use Storage Input or Storage IO blocks for this kind of setup and make sure that the input chest is only touching them and no other storage that is part of multiblock. Storage Input/IO can connect to multiblock, but they won't connect any other blocks through them.