The search algorithm scores each search result based on the number of matched terms. This scoring is correct only for either MetadataScope.USER or MetadataScope.SYSTEM, but not across both (which is the only exposed usecase.
This bug will be triggered if the search query has matches in both scopes. The code in question is DefaultMetadataStore.java#L371-L374. Since the search results are sorted by score in each scope separately, then merged into a set, the ultimate ordering may not be correct.