What you are seeing is 'ground water' either the water table in your yard has raised with rain/ snow melt or that water is not able to pass quickly enough through the ground and is temporarily 'puddled' under your pool. If the pool was full, the water under the liner probably wouldn't be able to push the liner around.

Re the missing water, were you pumping the cover off over the winter? A hole in the cover could mean that you were draining the pool while pumping the cover (but that's an awful lot of water and you probably would have noticed). A broken line at the current height of the pool water could be the culprit, hence my earlier suggestion to pressure test the lines. Has the water stopped at ~ the same height as the multiport? - this could indicate that the water was siphoning.

Thanks for the update, please keep us posted with the progress.