Do you have a puck auto chlorinator that has a black tube after your pump before the filter and then one after the filter for the return? If so in spa mode water will drain back into your pool unless you close the shutoff to the chlorinator. Not sure if this is your case but that's what happened to me once before figuring it out .
You sure it didn't get put into spa mode at all during the day, even momentarily? No one got in the spa?
Does your pump schedule end with the spillway running? I could see water backflowing to the pool if the pump is off and the valve rotates.