I was playing around a bit and mined a shaft in the hopes of finding lava at the bottom to test a setup, then I noticed I used the OD scanner instead of the OV scanner so I retracted all pipes and let it start a new and was later wondering why it stopped but left me more pipes over than before.
So I went down and saw that the mining head stopped before some flown in water. I then blocked the flow into the shaft and it instantly went on.
Hope this wasn't reported yet but searching for "miner water" didn't show anything.
Oh and it seems to ignore ores not from vanilla or IC.