I don’t get how leagues have CBAs with officials that require them to keep clearly incompetent officials.

The more egregious part is that they don’t, actually. The CBA they have with the refs assoc specifically lays out that the NBA has the sole authority to dismiss officials that they find don’t meet the standards and score below a certain threshold on end of season evaluations. There is absolutely an avenue to get rid of incompetent officials, the league just chooses not to.