No, I mean incorrect assumptions. It doesn't matter if we're talking research in industry or academia; doing research based on flawed (not simplifying) assumptions is bad science.
In my opinion the scientific authors doing the work are in the best position to judge what assumptions are and are not appropriate for their work. If the science is bad we expect the community to pick up on that via peer review or in a subsequent publication.
That sort of contextualizes your post as a long winded statement of "My job is hard".