It does, however, change the validity of the "peer reviewed" status the paper has received, and thereby undermines the entire reason this paper has gotten so much attention.
If the journal is not credible, has published unreliable science in the past, has a stated agenda, and does not have an above-board peer-review process, then it is no more worthy of trust than the World News Daily.
Undermining the credibility of the journal a paper is published in is fair game when the credibility of the journal is the only reason any credibility is assigned to the paper.