This has also been happening to me frequently. I have no clue how to fix it, or what triggers it. One time it happened when Kerfur was literal steps outside of my base, and other times it happens far away, so it doesn't seem related to a specific location. I just reload my save :/
Viewing post in Kerfur omega flesh pit + disappearance
for me it happened when i sent kerfur out to do reports, he went towards the lake (presumably towards oscar or something) and i heard a placeholder sound (kleiner saying fiddlesticks) and i couldn't pause for a while, i checked kerfur's camera and he was in the flesh pit
i tried to retrace his steps and found a blood stain, i assume that's where he disappeared