Excess average estimated identical-by-descent in genotype data
A clear negative association within an inbreeding coefficient suggests convergent evolution driven by shared selective pressure. There is an outside chance of purifying selection, or else balancing selection, but selection is the key word. The phenotype of the locus needs investigating, i.e. outside nearly neutral theory what is constitutes positive selection?
Allopatry caused by genetic isolation and genetic drift is your null hypothesis. However Darwinian positive selection is the alternative hypothesis.
I would be wary against suggesting contamination unless you've a clear suspicion this is occuring. I do accept that in human genetics its often difficult to avoid, particularly in ancient DNA type work. In this case you would need to try and control for it. The argument I would put against contamination is that 'genetic relatedness' is localised within the genome, whereas contamination would be a genome-wide phenomena.
Convergence is common within for example HLA genotypes (T-cell) loci between global populations.
You could perform formal tests for postive selection either within pop gen (the locus will associate with significant homozygosity) or phylogeny (point mutation).