Hey cloudy666,
Yes, this is a known issue with Excavator. Excavator's pathfinder and block breaker are two separate systems that don't really talk to each other, which can lead to odd situations like that.
Basically the pathfinder wants to go to a block on the top layer that's far away, while the block breaker doesn't know about that plan and instead wants to mine out the blocks under your feet that are much closer.
I don't have a fix at the moment, but it should be possible to make them cooperate better in a future update.