BuildCraft version: 7.99.22
Forge version: 14.23.5.2768
Link to crash report or log: N/A
Singleplayer or multiplayer: Singleplayer
Steps to reproduce:
It may happen if the quarry finds oil or lava. It will not remove blocks under it (which is expected), if you wait for the quarry to process a few layers and then remove the liquid, the quarry will 'forget' about the liquid and consequently the blocks under it, creating a column.
Additional information:
Above the blocks that are being ignored there was an 'oil font' or a 'lava font', I removed the liquids but I guess the quarry still thinks there is liquid above it.

In the meantime, break and replace the quarry. There's also a possibility that this is unfixable, because of the way block updates work. (Don't count me on that :P)

If u dont have a pump with the quarry it wont pass solid fuels (oil or lava etc) but it does mine thru water thou