Have you tried updating your school iPads to iOS 8 recently? If so, you will probably receive an error where iBooks can’t be installed. However, if you look on the iPad you’ll see that iBooks is actually preinstalled with iOS 8. The error message is there because Apple Configurator is trying to install iBooks but it is now already there… always.
To avoid this error message in Apple Configurator, delete the iBooks app from the list of apps with the minus button (don’t worry, this won’t remove iBooks from the iPad). Now click refresh and you shouldn’t get the error message again.
This might also be the case with apps like Podcasts etc.
More details to follow, including new documents in the Apple Configurator section of this site.