The contractor says that, under JCT Intermediate Building Contract 2009, it has no liability for defects appearing after the end of the rectification period. Is that correct?

Any defects that appear after the rectification period can still be considered breaches of contract. The contractor can still be considered liable for them up until the point at which the limitation period has expired. The employer is legally entitled to treat such defects as if the rectification period is non-existent.