He said he was going to fix the continuity errors that have plagued the series starting with X-Men: The Last Stand and perpetuated with X-Men Origins: Wolverine.
But there weren't any noteworthy continuity errors between the films as of The Last Stand
and X-Men Origins: Wolverine
, other than things like the less than perfect consistency between Logan's Origins backstory and Stryker's declaration in X2 that he gave Logan claws, the difference in Creed's appearance from Origins to X1, and perhaps the appearance of a human-looking Hank McCoy in X2, and these seem unlikely to be addressed by Singer. The continuity problems were caused by First Class
not matching up with the preceding films, TLS and Origins included. Continuity errors were not "plaguing" the series before then, but the films were being criticized for other reasons ( including differing from the source material in the comics ).