Recently there has been users merging items that by consensus should be kept separate. This is in bioinformatics where protein items has been merged with their associated gene items. It is likely the merging wizard that makes it too easy to merge.
In Magnus Manske's merging game it is not possible to merge two items that are linked AFAIU. It is then not possible to merge protein/gene as these items are usually linked by the "expressed by" property. Similar solution could be put into the merging wizard to warn users or to entire disable merging.
The issue has been discussed on the Wikidata mailing list, see threads https://lists.wikimedia.org/pipermail/wikidata/2015-November/007586.html and https://lists.wikimedia.org/pipermail/wikidata/2015-November/007580.html
(NOTE) Requirement: wbmergeitems shall not merge items that reference each other via an EntityIdValue in a main snak, qualifier, or reference, unless this restriction is explicitly overridden using the the `"statement"` flag in the `ignoreconflicts` parameter.