Make sure you tell it to ignore your search indexes and other SharePoint areas!
To be sure it is not hitting your index location, you can check where that is currently set by:
Central Admin -> Application Management -> Manage service applications
-> Search Service Application ->Search Application Topology (Modify)
-> IndexPartition/Query Component (Edit Properties).
Or via PowerShell, run the SharePoint 2010 Management Shell command:
"Microsoft strongly encourages the development and adoption of SharePoint Portal Server VS API-based antivirus solutions."
but the only one I can find for SP2013 is ESET…http://www.eset.com/beta/sharepoint/
PPS: I have heard that Symantec have a SP2013 aware thing in beta. Supposedly a separate server. Will know more in a month or two.