I'm guessing here so it could be a few things...
It could well be that the pad didn't dry properly as the waterproof layer will prevent drying through the bottom half (50% less efficient). This is after a wash or after it has been peed on - the liquid will only be able to dry/evaporate away through the top surface.
Or - if it is just
one of the pads - it could be that the waterproof layer in that pad has got a little hole or tear so liquid is seeping through and then pooling underneath. Fleece (a man-made fibre) isn't absorbent like natural fibres (cotton etc) so any water would be trapped underneath and just sit in a puddle. I guess the way to test that would be wash and dry the offending pad and then deliberately put it down onto a wet surface. Press it down - if any part of the top starts to feel wet that is where the water is seeping up through a hole. If it
all starts to feel damp all over your waterproof layer might not be waterproof enough! I'm remembering an uncomfortable beach picnic here - on a typically damp British beach - we thought we'd done well using a tarp under our picnic blanket but then had to walk back to the car past a
lot of people with very obvious wet bottoms!
My liners are fleece/absorbent layer (Zorb)/fleece so they can be used either way up. It also makes drying them after a wash much quicker. My pigs are on a hard tiled floor underneath though, so I don't have to worry about pee soaking in - it just gets wiped over each week. I use big homemade liners and then smaller versions on top (pee pads) where they tend to pee a lot, and switch them out as they need it which might be once a week or after a few days. TBH I sometimes just flip a smaller pad over and get another day out of it! I can understand why you included a waterproof layer but the problem here is drying. If I was on a different surface - like wood or something - I think I would rather line out the whole enclosure with something thick and waterproof like correx or lino (we can get off-cuts pretty cheap from carpet shops) and then just stick with fleece/zorb/fleece on top of that rather than worry about leaking liners. But then I bet your sewing skills are much better than my rough efforts
Good luck! Let us know how you get on.