Goniopora will commonly do this when under stress, it's often reffered to as a "polyp bailout." If under the proper conditions, it will live. I hate to be negative, but usually the bailouts do not live for a long time in the aquarium. If the colony was stressed, the bailouts have little chance of thriving in the same habitat that the stressed coral was in (unless the original conditions that the Goniopora was receiving was far from what was it was acustomed to).
I think a picture would greatly help, so we could see if this was a chunk, as stated above, that a fish nibbled off, or if this was an attempt to get to a better environment.
Goniopora usually has little success rate in captivity and very few make it past 3-6 months. They often prefer a nutrient rich environment, as they are found in shallow lagoons filled completely with nutrients and food.
Good luck!
Take Care,
Graham