@jhawkey the most recent version is 1.0.0 (if it's not appearing automatically, you can use Manuscripts > Check for Updates to bring the update dialog up). Here's also a direct download link for your convenience: http://updates.manuscriptsapp.com/apps/manuscripts/beta/download
Regarding the specific issue of the citation style for BMC Genomics. It's quite possible there's either an error in the citation style or our interpretation of it. I've made a note to look further into this. Thanks for giving a specific example!