I had recently ran into a case where a site collection was not created in the correct content database. Moving it to the correct database is very simple.
1) Open the SharePoint 2010 Management Shell as the SharePoint Farm Administrator
2) Enter the following command
Move-SPSite sitecollectionurl -DestinationDatabase contentdatabase
3) When prompted to confirm the move, type “Y”
4) Perform a reset of IIS using the iisreset command
You can now verify it was moved by viewing the site collections in the Central Administration site.