My understanding of what happened (and i could be wrong) was that the VCT cam gear was completely pulled apart, then when put back together it was done incorrectly which moved the position of the TDC mark. Then it was put onto the intake camshaft, all TDC were marked up correctly and the belt was put on. So it appeared the belt was on correctly, when looking at the TDC dots, but in fact the VCT cam gear was wrong.
Is that right? Because other than that explanation I don't understand how you can do it incorrectly, the cam gears can only be placed onto the camshaft one way and the dots can only align up one way.