I joined two objects together, but when I edit the object, they aren't completely joined I am currently making a bird in Blender, and I accidentally separated the wing of the bird from the body. After realizing I didn't need to separate the objects, I then rejoined them back together (control J). 

Now I am adding bones to the object, but when the wings flap, you can see a hole in the bird's body where I separated the objects. How do I completely join the wing back to the body so this hole doesn't exist?
You have two edge loops that overlap perfectly, one on the body, the other on the wing. To fix the issue, select everything, then press W and choose remove doubles.