The Palmerston rider finished second in yesterday's second leg of the series in Pietramurata, Italy, but extended her lead at the top of the championship.
The 21-year-old had led midway through both of the races.
However, mistakes proved costly, as she was forced to settle for a second and third.
Italian Kiara Fontanesi won her home event, with first and second-place finishes.
She capitalised on Duncan's fall in the first race and proved too much to pull in.
Duncan was able to get herself back into second, however, edging past Nancy Van De Ven.
The second race came down to who could make the fewest mistakes and again a fall hampered Duncan.
She had been riding at a blistering pace in the lead, before coming down and having to settle for third.
Livia Lancelot won the race, while Fontanesi was second.
It was enough for Fontanesi to claim the overall win, with 47 points, while Duncan trailed with 42.
While frustrated with the result, Duncan said there were positives to take out of the weekend.
``I put myself in good positions in both the races,'' she said.
``I was in the lead halfway through each race and made a silly mistake in both of them which cost me dearly.
``The speed was really good and I still have the red plate [for the WMX points lead].
``I have six weeks before the next round to learn and get better and, hopefully, come back swinging and in fine form for France.''
Having won the Indonesian leg of the championship, Duncan remains in first place on 83 points.
She is followed by Fontanesi, on 77, and Lancelot, on 67.
Duncan will remain in Europe for the next six months.
