I actually had the opposite problem. I had BME classes that were basically placeholders for independent study semesters and they had generic titles like "BME 192: Projects" or something like that. But because in the years past, people at my school apparently put down those courses as BCPM and had them approved, it set something of a precedent. So when I put them under engineering, they were verified as biology. Good thing my PI was very nice and gave me A's

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So anyway, to make a long story short, sometimes AMCAS goes by established precedent also. If a non-science department course was verified as BCPM in the past, then chances that it will be again is increased.
Edit: to be clear, my independent study project was basically a developmental biology project, so I guess it deserved a BCPM designation. But there was no way for the verifier to know that since I didn't specify what my project was or even its title.