Hello,
Sounds like your guess is correct. I believe the mother is alienating this kitten from the rest, due to it being underdeveloped or another illness.
Does the kitten have hair? Does it look like the other?
I would continue to put the kitten back with Mom if you can and continue to do so to see if the kitten will nurse. If it is underdeveloped and the mother will not nurse it, you can bottle feed it yourself and put it in a box or laundry hamper with towels and a heating pad on very low.
I hope this helps. If you need more information, please feel free to contact me.
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