BuildCraft version: 7.99.21 (all in one jar, with BC ore processing addon)
Forge version: 14.23.5.2810
Link to crash report or log:
Singleplayer or multiplayer: Singelplayer / Mining Dimension
Steps to reproduce:

1. Place a quarry and power it with a combustion engine, one wooden kinesis extraction pipe with an iron gate with trigger slots and an extra stone kinesis pipe between the wooden one and the quarry.
2. Set the gate to emit redstone when power is requested
3. Let the quarry finish
4. Once the quarry stops (at bedrock layer) - the engine is still running.
5. Braking the stone kinesis pipe (eg breaking the connection between the gate on the wooden k. pipe and the quarry) turns of the redstone signal as expected and the engine powers down.

Additional information:
I configured the mining dimension without lava lakes - so it can always quarry down to bedrock.

Aroma1997s-Dimensional-World-1.12.2-2.0.0.2.b86

Edit:
The 'lights' on the quarry are always black - so they can't be used to see if it has finished or not - one needs to look if it's still moving while consuming power.