>>1113828Possibly higher induced drag, higher wing structural mass, main spar not coresident with main landing gear resulting in more mass, those are the obvious ones.
But, you do have higher wing efficiency due to lift vortex recycling, more wing area within classical tarmac box size without folding, potentially thinner wings allowing even better efficiency due to higher aspect ratio, high set propulsion allowing larger fan diameter, and all surfaces contribute to lift.
There is an argument that a C-wing is better than a box wing, depending on the circumstances.