population admixture
Disclaimer, I am not an expert on admixture, answer is provided without any warranty.

It depends what you want to figure out. Why do you want to categorize the ancestry of the individual? If you analyze this origin of population X you should make a reference without population X and analyze all the individuals from the population with all the surrounding populations in the reference. However if you are interested in origin of a single individual, than the population X got to be in reference as well.

If your result will be that 90% of SNPs of your individual correspond to your population X, then it means that's a normal X fellow. Why it should be a problem?

-- edit --

I just found this preprint that highlights potential pitfalls in interpretation of STRUCTURE/ADMIXTURE results.