"But let us never forget, either, as all conventional history of philosophy conspires to make us forget, what the 'great thinkers' really are: proper objects, indeed, of pity, but even more, of horror."
David Stove's "What Is Wrong With Our Thoughts" is a critique of philosophy that I can only call epic.
The astute reader will of course find themselves objecting to Stove's notion that we should be catologuing every possible way to do philosophy wrong. It's not like there's some originally pure mode of thought, being tainted by only a small library of poisons. It's just that there are exponentially more possible crazy thoughts than sane thoughts, c.f. entropy.
But Stove's list of 39 different classic crazinesses applied to the number three is absolute pure epic gold. (Scroll down about halfway through if you want to jump there directly.)
I especially like #8: "There is an integer between two and four, but it is not three, and its true name and nature are not to be revealed."
"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.