This could, as Adeese mentions in his answer, mean that one Quarian is not enough to extrapolate a face for 'any Quarian' personally, though, I took it to mean that you thought well enough of Tali that you did not associate her with the Quarians willing to commit genocide on the Geth. According to Murgatroid99 in the comments below, the line is something close to : 'Then your memories of that Quarian do not map to our historical data'. When I answered that I had indeed seen one Quarian unmasked, Legion replied with something along the lines of 'then you must not associate that Quarian with the ones you are seeing'.

I however contend that this is NOT a plot hole : Shepard commented upon this fact, with his guide (Legion, in my case) asking if he had ever seen a Quarian without his mask. Playing through the game with my own ME2 save where I romanced Tali, the scene still played out as you described (with masked Quarians). Adding my own answer since none of the others feel entirely correct to me )

Tali face mass effect 3