If you follow Microsoft best practice to migrate site collections from SP2010 to SP2013, you need to upgrade the migrated site collections to “SP2013-evaluation mode" first. During that mode, SharePoint will use your SP2010 site existing data to create a new site collection with SP2013 code (Master, style, new control, etc) with a suffix “-eval" as the site collection name.
It is a great feature. However, if you setup crawling against this eval site, there will be chance the index messed up.
In my test environment, I have several site collection run in evaluation mode. I setup content sources separately crawl each site collections. But end up the index mess up each other.
i.e. I have site collection A and B
I setup content sources A and B to crawl only A and B.
End up content source A contain both A & B’s item and source B contain only the landing page.