My guess would be politics. Congress in the US is democratically controlled while the Senate and Presidency are republican controlled. The current administration is fairly anti-Muslim and has ignored the Uighar issues entirely, the current administration likely told the State Department not to issue the visa.
The current administration appointed a Uighar-American as National Security Council Director of China to advise the president on China issues. However, this appointment was ignored by US media, for reasons we can only speculate. While much of the administration's response to China issues has been characterized as "heavy handed" by the same media, that leadership is responsible for influencing the EU to take a similar approach. There's much of Trump I don't like, but I wholly approve of that administration's actions regarding the whole of China.
However he also supported China's anti-Uigher policy in secret remarks[1] to President Xi. There seems to be a hidden agenda at odds with the public agenda.
This is why it's important that the White House challenges China for the right reasons with the right strategy. Trump is certainly the most anti-China president in years, but he often contradicts himself and frames it with racist, partisan, and protectionist rhetoric, actually damaging human rights-based anti-China opposition. Not to mention he's intent on weakening the levers of soft power that the US has traditionally used as he damages alliances and withdraws from global organizations like the WHO.
It's not enough to be publicly anti-China. Effective leadership demands a focused message, effective coalition building, and unifying rhetoric where Trump has turned it into a partisan wedge like everything he wades into.
Emissaries and consulates are typically ran by career government employees in the US but their operation is overseen by the Secretary of State (a presidential cabinet member) and the State Department. So the presidential appointee has a lot of power over what does and does not happen at consulates/emissaries.
