@The Muffin Man
If that is your real name, here is the reason.
TFS outputs stuff into a common bin directory, in which all of your files will be dumped to, with exception of your websites. Which should be in a _PLublishedWebsites like directory.
You will need to configure TFS Build Workflow to dump the projects into separate build directories. I believe with newer versions of TFS this is easier, however it will require you to open and edit the TFS Workflow you are using to build your software.
This is a frustrating aspect of TFS Build because you will need to checkin the TFS workflow and run it to verify that has fixed the problem.
I found this
In TFS 2012 / .net 4.5 you can control this behaviour by passing an msbuild argument in your build definition /p:GenerateProjectSpecificOutputFolder=true
While i liked the whole notion of TFS i think the other more mature build servers (TEamCity, Go.cd, Jenkins) are really polished in this respect because they just use MSBUILD. So its very easy to test and tweak, because the result will be the same on the build server as it is on the individual developer machines. /rant.