They are "fixed" by extending the evidence base for decision making well beyond raw clinical trial data and publications on them (none of which ever translates into real world practice outcomes anyway).

In important instances (such as expensive meds going to large numbers of people) the payer will commission their own research e.g. through NIHR https://www.nihr.ac.uk/

There is a whole field of "value of information" now to estimate how incorrect information would affect a decision and whether it warrants research investment (which covers publication bias - e.g. how many unpublished studies showing no or negative effects would there need to be to change the decision)