Make sure you contract is well defined to avoid scope creep (Ie, constant changes to site plan as financing, anchors and tenants shake out)
Also, keep good documention of your correspondence with architects. There maybe more than one for varous buildings (if a large site). There is a tendency to keep changing footprints and locations of utilities. Also door locations which affects your ADA requirements. This was very labor intensive for me on one project.
Developers will naturally want more available land for development, rather than detention if it's required. This tends to cause conflicts as they squeeze detention into smaller spots. Make sure you have a paper trail exlaining increased costs due to retaining walls and sheer pond walls if they tell you 'it just has to work in this area'. Also, you'll find they want detention ponds way out of the way, but oftentimes not condusive for detention (Ie, located at the uphill side of the site)
Truck loading docks are sometimes problematic. At first they won't be there, then later the architecural footprint includes them. Recessed loading docks need to be drained, so beware of having to extend a storm line, or go to a pumped system with added costs.
Be very very carefull about matching grades of architectural drawings to your finished grades on the civil plans. They will use a relative datum to a finished floor of 100, so you have to do some math. When they don't match in the field, the finger pointing begins.
Restaurants will need grease traps. Be sure to find out who is responsible for their design. Usually the MEP, but they are located will outside the buidling, so their could be some overlap.
You may get your cut and fill to balance on paper, then the actual dirt guy looks at it and says 'we show a net cut or fill of so many thousand yards!!'. Then, to balance, they will want to raise or lower the site by some constant incriment, say, 0.63 foot raise. Make sure you anticipate how to deal with this, aside from you changing every spot elevation you have. Your driveway slopes will be affected, cover over shallow utilites, a whole host of items.
Each one of these items burned me at one point. Live and learn. The key is to anticipate the items that will burn you and deal with them proactively.
Good luck.