Vortices are essential to angular momentum in quantum systems such as ultracold atomic gases. The existence of quantized vorticity in bosonic systems stimulated the development of the Gross-Pitaevskii mean-field approximation. However, the true dynamics of angular momentum in finite, interacting many-body systems like trapped Bose-Einstein condensates is enriched by the emergence of quantum correlations whose description demands more elaborate methods. Herein we theoretically investigate the full many-body dynamics of the acquisition of angular momentum by a gas of ultracold bosons in two dimensions using a standard rotation procedure. We demonstrate the existence of a novel mode of quantized vorticity, which we term the phantom vortex. Contrary to the conventional mean-field vortex, can be detected as a topological defect of spatial coherence, but not of the density. We describe previously unknown many-body mechanisms of vortex nucleation and show that angular momentum is hidden in phantom vortices modes which so far seem to have evaded experimental detection. This phenomenon is likely important in the formation of the Abrikosov lattice and the onset of turbulence in superfluids.