Furthermore, it doesn't appear that they're looking at whether the reason the paper was cited was the subject of the failed replication.

To analogize to the legal field, which they mention in the article, if a case I cite is good law on one point of law, but no longer good law on another I may cite it as _Plaintiff v. Defendant_, 123 F.3d 456 (1998) (reversed on other grounds, _Defendant v. Plaintiff_ 78 S.Ct. 910 (2000))

Just because one finding in a paper wasn't replicated doesn't mean that the paper can't or shouldn't be cited for other findings.