3 green dots still illuminated for abyss after full clear

I have killed all of the monsters for an abyss pit but there are still 3 green dots illuminated. I have checked every nook & cranny and ran any bonus content in the vicinity.

Bug Report ID: #1569401655 - right when it happened

Bug Report ID: #1523560453 - after I fully cleared the map down to 0 monsters. Screenshot attached.