The Wiki article seems to dispute this claim...
"A complex LCN [low copy number] DNA result which appeared to have originated from at least three people was obtained from cellular material recovered from the luggage compartment section ... Within the DNA profile of Madeleine McCann there are 20 DNA components represented by 19 peaks on a chart. ... Of these 19 components 15 are present within the result from this item; there are 37 components in total. There are 37 components because there are at least 3 contributors; but there could be up to five contributors. In my opinion therefore this result is too complex for meaningful interpretation/inclusion. ... The individual components in Madeleine's profile are not unique to her; it is the specific combination of 19 components that makes her profile unique above all others. Elements of Madeleine's profile are also present within the profiles of many of the scientists here in Birmingham, myself included. It's important to stress that 50% of Madeleine's profile will be shared with each parent. It is not possible, in a mixture of more than two people, to determine or evaluate which specific DNA components pair with each other. ... Therefore, we cannot answer the question: Is the match genuine, or is it a chance match"
Doesn't seem to dispute it, just seems to clarify that, without all 19 markers, there is a chance that they do not all belong to Maddy. That chance? 1 in 1000, apparently.