There's probably a mix of both. At some point, most people probably realize that there's something fundamentally wrong - but by then, they're a few decades in and too much of their career and personal life depends on it being true, so openly changing course is very daunting. When your identity and career depends on something wrong being considered true, you have no incentive to point out problems, and every incentive to mislead.
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Of malice vs stupidity, I'm pretty certain it's stupidity. Or more precisely, self-delusion.
The story of Millikan's oil drop experiment replications and also James Randi's (and CSICOP's) battle with pseudo-scientists convince me of this.
There's probably a mix of both. At some point, most people probably realize that there's something fundamentally wrong - but by then, they're a few decades in and too much of their career and personal life depends on it being true, so openly changing course is very daunting. When your identity and career depends on something wrong being considered true, you have no incentive to point out problems, and every incentive to mislead.