The column on the left does indeed overlap the black outline of the center square. This was erroneously charted in black.
Center Specialty Stitches
Column Overlaps Center Square
Column Overlaps Center Square
The specialty stitches on the chart may appear in different colors (eyelets in grey and dense Rhodes in purple); however, the instructions state to use GLO 071 - Winter Brook for both.
In general, Martina uses "placeholder" colors when making the pattern and does not necessarily change them after her final color selections. It is best to use the written instructions as the authoritative source if there is a discrepancy.