That's a pressurised pond filter there surely, seems like a Hozelock model from what I can see?
It looks like they've not washed the gravel before adding it. However 'washed' the supplier says it is, gravel always needs a good hoseing down before use IMHO. However, there does seem to be a lot of sediment collecting on the liner and it's not all settled out yet. Where is the pump placed, is it at the far end of the pond, it should draw water 'through' the pond and not just be close to the waterfall?
Can I ask, were they a professional pondscaping team? I can see a few probs at the mo. The soil will wash into the pond if the angle of the surrounding ground is flat or slopes towards the pond....is it sloping away?
The liner should have been pulled much tighter and flatter around the edge, that way it could have been disguised better by placing the edging rocks to slightly overlap the edge of it.
Some kinds of liners can actually degrade or go brittle and split if there's sufficient sun shining on them, despite the sun being sometimes elusive here in the U.K., plus being exposed they can suffer damage and get punctured more easily....and it doesn't look quite right as you said.
The water level should ideally come up to the underside of the surrounding rocks, both for protection and looks. They need to be turned so that their straight edges slightly overhang the pond edge, can easily be trimmed to fit together, jagged edges then protrude into the soil etc.
Was the waterfall and other rock work washed down in any way after it was jointed? The runoff from the new mortar could also be contributing to the cloudiness. It should ideally have been washed along with the gravel till everything run clear, the dirty water emptied so you start with everything clean.
If it were my pond, I would seriously consider getting them back to do some tweaks in order to get your pond looking better especially as you don't sound happy with it. I certainly wouldn't accept their work as it stands. Yes the water will clear given time, but I think there are some other issues that they should be made aware of. It's going to be a great natural pond for creatures though. Where are you situated, no need for exact location, just out of interest? I'm in Staffs Moorlands.