Why does your belly button piercing have a indented at the top ball?

That sort of thing happens if you weren't pierced at an ideal angle (i.e. in this case, probably too much of an angle; piercings work best when they enter and come out perpendicular to the skin). If they come out at too much of angle relative to the surface of the skin, then the skin may try to grow over. It also is possible that your piercer did a perfectly good job, but that's just what your particular body does in reaction to a belly button piercing.

Or, wait a minute... Since you say it's growing over the BALL, and not the other part of jewelry (I was picturing a ring; I forgot for a minute that most women don't wear rings in their belly button piercing), it sounds like the only way that that could possibly happen is if your jewerly is way too small/tight! Get yourself some jewelry of the proper size and that won't happen! If you got it done recently, it might be the case that the jewelry you have is the proper size for later but not big enough to accommodate current swelling.