"Study limitations" is standard language in epidemiological papers, so that's not a surprise, nor a condemnation.
Further, to my knowledge it is known that "case zero" (i.e. the zoonotic event) did not occur at the Wuhan market, specifically because there was already sequence divergence in early cases.
However, that doesn't prevent the market from being the main source of the outbreak. There's no evidence for any other source.