Mendeley and Scopus use different information to generate their respective views on your publications.
Scopus is an independent database that indexes journal articles. It attributes authorship to these articles using a sophisticated algorithm, but it may occasionally make errors such as misattribution or failing to include a publication. As an objective public record, Scopus welcomes correction of factual inaccuracies through the Scopus Feedback Wizard.
Mendeley associates your publications with you only through the My Publications folder. This enables you to present either a full or partial view of your publications on your showcase profile. You can add or remove publications as you see fit.
Because the sources of information are different, they need to be managed separately. Removing publications from your My Publications folder will not remove them from Scopus, and vice versa.