VortiK's Deep Core Mining has a small chance to create an infinite ore patch on a depleted "normal" ore patch. These require special equipment from that mod to be mined. When that happens, the miner currently mining that spot won't be marked for deconstruction.

A quick glance at the code makes me think has_resources(drill) is the culprit here. The drill has a resource, just not one it can mine. Checking for equality with the resource that generated the event might be an option, but that won't work if a miner overlaps two different resources.
Can one filter for only mineable resources?
The only other way I could think of is to specifically exclude the Deep Core resources from checks.

Bottleneck shows a red dot, so it should be detectable if the miner in question is resource-starved.