When connected to my Salesforce Sandbox / Dev Org I get the following errors:

Looking at the actual package file it seems like there aren't any references to these ConnectedApps (Eg Chatter_desktop, Dataloader_Bulk and so on)
Is Force.com IDE expecting to see these references?
Edit: Ah I see there's a package.xml for each referenced package. Eg this is the package.xml for Chatter Desktop:
<?xml version="1.0" encoding="UTF-8"?>
<Package xmlns="http://soap.sforce.com/2006/04/metadata">
<fullName>Chatter_Desktop</fullName>
<apiAccessLevel>Unrestricted</apiAccessLevel>
<namespacePrefix>sf_chttr_apps</namespacePrefix>
<types>
<members>Chatter_Desktop</members>
<name>Application</name>
</types>
<version>30.0</version>
</Package>
I've noticed that if I go to a sandbox org webpage and go to
Administration Setup > Manage Apps > Connected Apps
And then click edit on any of the apps I get an Internal Server error. Never good.
I've seen this with every sandbox/dev org I've created. It doesn't seem to cause me any problems, but can anyone explain what these warnings mean?