Have you experienced opening a library and noticing the pads do not overlap, but when you try to incorporate that library into your PCB design, you notice the pads overlap? 

What you are experiencing is the EAGLE's feature with the Annular Ring/Restring function. It wants to guarantee that the annular ring around your plated through holes is thick enough to produce reliable connections on your PCB.

In order to use the component, you will have to adjust the DRC > Annular Ring settings to allow the settings in the library to win out. 

You can read more about how restring works here. The ring values purely depends on your design preference so it's really important to read and understand how it works before setting up your final values.