The master problem is an LP (not MIP)? If so, I don't think duplication should be possible in theory. The subproblem optimizes what would be the reduced cost of the new column in the master problem, and if the column already exists, its reduced cost must be zero or have the "wrong" sign.
So (assuming this is an LP), you might want to check whether your comparisons of subproblem objective value to zero allow for sufficient rounding tolerance, and maybe see if your subproblem (or master problem) has a bad kappa value (condition number), indicating possible numerical instability.
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