Wes,
Report the problem to your pool builder.
Sounds to me like a valve was moved that may have blocked off the water flow for a moment. Did something happen just before the problem? Did someone move a valve, did you change between the pool mode and spa mode? Anything?? Were people swimming at the time? Did you turn a cleaner on or off??
I would just reboot the whole system and see if the problem returns. To do that just push the reset button on the main panel. It will not erase anything; it is like rebooting your PC.
Show us some pics of your equipment pad and if possible, the label on your IntelliFlo pump that shows the pump's model or name.
Thanks,
Jim R.