From what I can tell, the rock crew dumped the left over motor into an open trench with exposed plumbing. Should I be concerned or is this standard procedure? It looks like several feet of plumbing is fully encased in mortar.
I wouldn't worry too much. Utilities in commercial construction are sometimes encased in concrete. This is mostly to protect them from damge later from somebody digging. If the tractor hits the concrete they have a chance to stop and see what it is instead of breaking it. It will help protect it from movement over time, but will make it more difficult to get to if you should have to get to it later.
It'll protect it (somewhat) from having a stake from the formwork driven through the pipes when the deck is being put in. I've heard this is too common and because the deck isbeing poured right after is not known until it is too late.