I would mention it to the neighbour and ask them to keep an eye on the dog until the fence is up.
I would not ask them to clear up the exisiting poop (and it sounds as though you have dealt with than anyway) but it sounds as though they probably have not noticed, or don't see it as an issue, so I think a polite
"You probably haven't realised, but Fido has been coming into our yard and doing his business - could you keep an eye on him, til the fence is finished, to make sure it doesn't happen again?" (If appropriate, you could also point our that your yard isn't dog proof, so that it is part concern over Fido's wellbeing as well as part you don't want dog dirt in your yard.
Alternatively, if you don;t want to speak to the neighbour, consider buying some of those 'get of my garden products and putting them down, and/or putting a temporary barrier across the gap.