A. The first question is how did they figure in those two factors? Self selection is a real factor. Let’s use UIUC again, and compare it to U of Minn. UIUC’s acceptance rate is, officially about 65.6%, while UMN’s is 44.6%, so it would seem that UMN is more selective than UIUC, right? However, the middle 50% of ACTs of UIUC admitted undergrads are 27-33 versus UMN’s 27-32. Engineering UIUC - ACT 32-35, Engineering UMN 31-34. While using both ACTs and admission rates can deal with this somewhat, it depends on how each factor fits into the rankings.
B. It doesn’t talk about departments. For example, the acceptance rate of UIUC is pretty high, however, if you are trying to be accepted into their College of Engineering, your chances aren’t any better than if you were applying for an engineering degree at, say, U of Mich.
C. It’s all a popularity contest. Sometimes schools are popular because they are Really That Good, like Harvey Mudd or MIT, and sometimes it’s because they’re really good at advertising and branding, like Harvard.