I suspect this is caused by https://issues.sonatype.org/browse/NEXUS-17884. Please feel free to vote on that ticket.
@jan Yes running the yum rebuild metadata task does recreate the metadata files that are stored in the repodata folders. Also uploading a new RPM or deleting an RPM will trigger a rebuild of the metadata for the associated repodata folder. Was it a source RPM that caused this for you? If so removing just the source RPM should suffice?