If your paper had a formal correction, then this is not a mistake: your paper will be listed on PubMed twice.
In short: it’s because the formal correction counts as a different publication. On the PLoS ONE journal site, the correction of the error will be integrated into the original article and this correction will be announced via text in a red box at the top of the article page; however, in PubMed, the original article and the corrected are listed separately.
In more detail: if a published paper contains a major error, we issue a formal correction to fix that error, and the formal correction has its own DOI, or Date of Original Issue, from PLoS ONE. The formal correction then receives its own, separate entry in PubMed in order to link to the original document. The corrected entry will contain the word “correction” in its title, while the original will not. PubMed mandates that the original and the correction must both be entered in its database, as you can see here.
Please note that your corrected paper will show up only once in PMC (PubMed central), because the correction will be embedded in the PMC entry.
If you discover an error after publication and you feel that it’s important that your paper be listed only once in PubMed, you have two options. First, you can request that PLoS issue a minor correction, which will appear only on the manuscript page and not on PubMed; alternatively, you can request a republication, although this option is only available to you if you catch the error 48 hours or less after the date of publication in PLoS ONE. An important proviso: it’s ultimately up to the PLoS Publication department to decide what type of correction to issue, so please understand that while we will do our best to accommodate your requests, we’ll also need to keep journal policies and procedures in mind.
As you can see, the corrections process is a little on the complex side, even if you have a PhD like many members of the PLoS community do! Since PLoS ONE doesn’t have an author proofing step, let me put in a plug here to remind you to double-, triple-, and quadruple-check your paper before you approve it for publication.