There could be several causes for this.
You did too much too soon: If you are new to inversion, your body is not used to being inverted (chances are you haven't hung upside down since 2nd grade!) By inverting too much too soon, you are probably going to be a little sore. You can liken inversion to beginning any new exercise program. If you over-do it on the first day, you will probably pay for it later!
You returned upright too fast: When inverted, your vertebrae have a chance to separate and the discs can decompress. This action reduces pressure on the nerves that run through your spinal column. When you ascend (return upright) on the inversion table, your spine "re-compresses"-the vertebrae return to their normal position and the pressure on the discs increases again. If you come up from inversion too fast, you might place sudden pressure on the nerves that run through the spine, which can cause some pain. Instead, you should invert to a mild angle (30-40 degrees) for a just few minutes. Come back up only to the horizontal position (lying flat). Remain horizontal for several minutes to allow your spine to slowly re-compress. Then slowly come up the rest of the way.
Always keep in mind that if you experience extreme pain, or if you always experience pain while inverting, you should discontinue inversion until you have had a chance to talk with your doctor.