The military "got distracted" at the beginning.
Is it not just that most countries do not see much of a threat from an aircraft at that altitude so quite possibly 'muted' them on their display to avoid clutter, leave them for the civil ATC people to look after.
They could see their biggest threat as low level flights being used by insurgents or smugglers of various sorts.
An aircraft at that height without transponder could also be the Americans up to no good so best to not get involved.