"These situations sound like there is a much bigger problem than the elementary error, perhaps that the people involved just don't care about seeking truth, only about having a routine."

Well, a large part of it is funding/bureaucracy/grants. I tend to thing that's the main part in many of these fields. Look at Taubes's Good Calories, Bad Calories for a largely correct history of how the field of nutrition went wrong and is still going at it pretty badly. You do have a growing number of insiders doing research not on the "wrong" path and you did all along, but they never got strong enough to challenge the "consensus" and it's due not just to the field but the forces outside the field (think tanks, government agencies, media reports). So even being published and well-known isn't enough to change a field.