Yes, I agree that they were not intentionally hidden by Bulgakov. Maybe instead of "clues" it would be more accurate to describe them as things that a modern non-Russian reader might not pick up unless some additional context is provided.
It occurs to me that you hit on one of Bulgakov's juxtapositions right in your first comment which can be a handy cue when there isn't a footnote -
"vanish one after the other as if by magic"
When the narrator suddenly feigns ignorance, is vague, evokes unclear, possibly supernatural forces at play - he's generally talking about things like the state terror or other entirely humanly-wrought events and matters.
When he talks about the actual supernatural - the devil and his retinue - he has no trouble at all following them around and describing their actions and their consequences precisely.
