Well, I'm no expert but, if you felt the need to line your main pond then it seems logical that you had reason to believe your soil might leak so, your pre-pond is bound to have the same soil with the same problems. Water weighs something and creates pressure so, maybe it just filled up to the point where the pressure is forcing your pre-pond water to find a place to leak.

Just my guess...

If you're too scared to throw that bait where the fish are, why did you tie it on?