These pads are smaller than the device's solder balls and are located far enough away from the individual solder balls that they will not cause shorts during reflow. These bumps are made of high temperature solder that will not melt during a regular reflow process where the peak reflow temperature does not exceed Altera's specified peak temperature (220 ºC).
You should ensure proper alignment of the part during pick-and-place by aligning the part based on the package outline rather than the location of the balls. Make sure that the thickness of the solder is not too high. If the solder is too high, it will cause shorts from the solder migrating to other balls as well as the ground pads.