In this letter we use high resolution scanning transmission electron microscopy to study epitaxial YBa2Cu3O7−δ (YBCO) nanocomposite thin films. We find that twin boundaries (TB) in YBCO nanocomposite thin films are disturbed by the presence of secondary phase nanoparticles as well as by intergrowths. Secondary phases promote the nucleation of TBs and, at the same time, result in bending, decreasing and changing the TB's spacing. On the other hand, the local strain ensuing from the partial dislocation associated to Y248 and Y125 intergrowths break the vertical coherence of TBs. This interaction results in a complex domain structure where twin boundary coherence is no longer satisfied and twin spacing is reduced down to a few nanometers precluding vortex channeling at low temperatures.