I conquered a village that had been used to settle another village. Now in my residence my first slot is occupied by that village. A bug I'm guessing? Any way to remove that village from the slot, or for that matter to get it assigned to me (2 for the price of 1 ;-)?

Conquering
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That's intended. Every non-starting village needs to take up an expansion slot.
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So how do I free up that slot? Or is there a way to take over the village?
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Hello
if you chief a village, you have to use a slot (or 2 if it's a city). So you can free up a slot in the residence of a village but that slot has to be occupied in another residence in another village. The other possibility is that someone chiefs your village so you will have the slot free -
Meh