I have been plagued by this problem over the past month or two. It didn't hurt anything – it was just annoying. The problem exhibited itself in both Xcode's 6.4 and 7.
I finally fixed it today by inserting the following lines into our project's info.plist:
<key>CFBundleIcons</key>
<dict/>
<key>CFBundleIcons~ipad</key>
<dict/>
Actually what I did was from the project settings' General pane under App Icons and Launch Images, I changed the App Icons Source from my asset catalog to "Don't use asset catalogs" and then changed it back to "Use Asset Catalog". Xcode then modified my asset catalog by inserting a 2nd entry for AppIcon, but I just rolled that change back using my git client. The change to the info.plist (shown above) I left in place, and this solved the issue for me.