There is a point where most the inhabitants of a shared flat vanish one after the other as if by magic, leaving only one of them behind.
Luckily, the footnotes point out the tiny clues in the text that tell the whole story: that tenant had denounced all of his flatmates to the secret police so he could keep the whole place for himself.
They're not really 'tiny clues' - this thread makes it sound like this stuff is some set of subtle veiled hints and allusions. It's certainly possible to miss if one is unfamiliar with the historical context and it's worth getting a well-annotated edition but it's hardly the intent of the author - there are lots of places where it's quite explicit and overt. The book itself could not be published when it was written and when it was originally published, many of the more obvious references to repression were edited out.
I happen to be reading the novel at the moment, so it was easy to find an example. In this fragment, the master recounts the last time that he saw his loved one. The sentences are spread over 3-4 pages:
“This was at dusk, in mid-October. And she left. [...] A quarter of an hour after she left me, there came a knock at my window [...] Yes, and so in mid-January, at night, in the same coat but with the buttons torn off, I was huddled with cold in my little yard.”
Just like that, three months have vanished. Those missing buttons are the only indication of where he spent those lost months: it was customary to remove belts, shoelaces and buttons from those held for questioning by the secret police.
That's a wonderful example and no, they aren't. To a contemporary Soviet reader (or a modern one with a bit more context), it's crystal clear who the 'they' knocking on the window in the middle of the night are. In fact, such readers would have a pretty good idea where things are headed the moment the new 'friend' Mogarich appears and is described. And after the knock but before the buttons, our knowingly winking omniscient narrator suddenly disappears, stops being omniscient and refuses to tell us what happened! The buttons are a nice detail at the tail end on which to hang an explanatory footnote, perhaps, but not some hidden clue, left in there for readers to suddenly slap their forehead and say 'Aha!'.
It's a multilayered work and, stylistically, Bulgakov is often a circumspect narrator. But the repression bits are not some particularly deeply hidden layer at all. You're barely a few pages in when Ivan suggests Kant be sent to the Solovki, one of the OG Gulags. The very title of the first chapter is a reference to the paranoia and legitimate fears of the period.
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.
Luckily, the footnotes point out the tiny clues in the text that tell the whole story: that tenant had denounced all of his flatmates to the secret police so he could keep the whole place for himself.