BuildCraft version: 7.99.13
Forge version: 14.23.1.2565
Singleplayer or multiplayer: multiplayer
Additional information:

Hi,

My quarry try to destroy water flow so this stop quary. I think quarry must ignore water and water flow or directy break water block.

I don't know if is realy a bug or if is a feature but i think is a bug.

Screenshot :

yes it should ignore flowing water, the quarry already does this when digging but apearently not for clearing the area, for now just get rid of the source blocks yourself and it'll finish setting up to start digging