As Buddha said of his own teaching, "Eso Dhammo Sanatano," even his supposed "critique" of the Vedas was limited to criticizing its mere recitation and mere belief in a creator.

The trilakshana are not necessarily in conflict with the traditional Hindu views of an Atman, if you take the Atman to be one in all sentient life (hence not a self at all) and consider "Buddhanature" to be related to the Atma idea - though Buddhists would maybe not be happy about that comparison...