So, I know I'm kind of late on this - but I think I know the solution to the major continuity error in TDAS.
Gwen continuously claims that she and Duncan never kissed while Duncan and Courtney were dating. The first time they kissed was in Greece's Pieces, when CxD was still happening.
Though, the second (and somewhat, "offcial") kiss between Gwuncan was in The EX-Files. This is when Gwen and Duncan were actually dating after Courtney broke-up with Duncan.
So, we can presume that Gwen is trying to deny the fact that Duncan cheated on Courtney with her, not the fact that they kissed while Courtney and Duncan were dating.