With the cover touching the water the pump could have sucked up some of the pool water.
My hypothesis comes my best friends pool. They cover it when they "close" it to help wiht the leaves and stuff. It was trying to overflow one year her husband put a pump on the cover and forgot about it.....when he remembered the pool was half empty!
Before you open PLEASE look down at my signature for the best kit out there. TF-100. The money you spend on it will save you SOOOO much money at the pool store. We even have videos on how to do the tests!
Believe it or not this is my 4th pool in the past 13 years (don't ask) and not including the pool I had growing up. I absolutely suck at the water management and dealing with chemicals. I usually walk into the pool supply place, have them test the water and walk out with $300 in chemicals. As of now all I have is a few pounds of power chlorine in the shed.