There's a popular baking story out there. Apparently, if you're cooking muffins you should fill your unused cups with water. According to the story, if you don't fill those empty cups with something (either batter or water), your pan will warp and the muffins will cook uneven.
Is this fact or fiction? Without a doubt, it's completely wrong. The way muffin tins are designed, the contents of individual cups don't affect the quality of the other. They are generally spaced far enough out. If your muffin tin warps, that's a sign you may need to step up the quality and buy a new one.
There is one scenario where this might be useful: if you greased all of the cups but didn't use them. Baking just the grease would be difficult to clean up. Feel free to fill it with water in that case just to keep cleaning simpler after the fact. Otherwise, don't worry about it. Filling those empty cups is just an unnecessary step.