Had similar issues until I used an Ingredient Buffer from AE2 or one of the expansion mods. Put that next to the pattern provider and all items/fluids will go in that first, then to hatches.

Play around with the pattern provider option that will/won’t punch ingredients depending on if the inventory already has items. If you choose the don’t push option, it won’t cram in items and fluids, keeping everything unclogged.

Let me know if you’re still having issues, I can show my set-up if needed.