Hi Tahir,
It's just the way that it happens to pick the first 3-level column. In this case, Fit Model would use those 2 replicates for lack of fit.
Another option is to add an additional 3-level factor, create the design, and drop the first 3-level column, using the second instead (this design shouldn't have any replicates).
Yet another choice is to bring the same factors into Custom Design, which may give you a different design structure.
Hope that helps,
Ryan