One quirk I've noticed about the Void Upgrade is that it uses fuzzy-matching (ignoring damage values) by default. This means that, as an example, filtering stone will also match diorite, andesite, and granite, as they all share the same item ID.

This would feel better in reverse, when the result is voiding items, a fuzzy match may create problems.
Imagine a mod which groups all of it's basic resources into a single item ID. If you want to void the annoyingly common resource, you'll also end up voiding the valuable ones!

My suggestion would be to change the existing Void Upgrade to a "Fuzzy Void Upgrade" - to maintain current functionality when people upgrade.
The recipe could be the same, except add wool to the 4 corners, or replace the black dye with black wool.
The current recipe would instead craft a new "Void Upgrade" (or "Precise Void Upgrade") which uses precise matching.

Thanks for the suggestion!

Yes, this is a great idea. Currently I would ideally like to have a basic/exact, fuzzy, oreDict, and advanced (all 3) matching for a number of filters, but the internal code doesn't currently allow for that much flexibility. My plan is to refactor it so that I can do the above, which also obviously includes your suggestion.

aah... I was wondering why my diorite was suddeny disappearing when adding the stone to the void filter.

Add Precise Void Upgrade