Has there ever been a manned space flight to orbit directly over the Antarctic?

No, there have been no manned spacecraft with polar orbits.

Part of the reason for this is that polar orbits are fuel-expensive - it takes more fuel to get to such an orbit as the launcher is not taking advantage of the earth's rotation. If you don't have to, you don't do it.

Another reason is that there's a radiation hazard due to the effect of the magnetic poles. The poles attract solar and cosmic particles - the effect that causes aurorae - and this would put astronauts at unnecessary risk over continuous orbits.
 
Manned flights go east / west, so I don't believe any have ever passed over the Antarctic.

Of course, many polar orbit satellites have been used, since it allows an earth observation satellite to pass over the entire surface of the planet eventually.
 
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