A Bose-Einstein condensate in a tilted double-well potential under the influence of time-periodic potential differences is investigated in the regime where the mean-field (Gross-Pitaevskii) dynamics become chaotic. For some parameters near stable regions, even averaging over several condensate oscillations does not remove the differences between mean-field and N-particle results. While introducing decoherence via piecewise deterministic processes reduces those differences, they are due to the emergence of mesoscopic entangled states in the chaotic regime.