When using the advanced search to add in my New Phyrexia cards I noticed that their is bug in the way your filter is working.

To reproduce the bug configure your advanced search like this;

Edition --> New Phyrexia
Rarity --> Uncommon

The following two cards show up for me on page 3;

http://deckbox.org/mtg/Phyrexian%20Hulk
http://deckbox.org/mtg/Evil%20Presence

In NPH both of these reprints are commons. In all of their multiple prior editions both of these cards are uncommon.

My guess is that the advanced search is using "rarity" criteria as the first search against the database and then applying the addition.

Could be wrong though!

This is working as intended. The filters are independent of each other, so if a card was ever uncommon, it will show up, even if you have selected an edition where it was printed as common.