Our GC Alon’s response to a discussion on Houzz about stucco:
1. Yes, stucco can be painted (if you choose to do this, make sure to use the right kind of paint and prep)
2. Yes, if you paint the fresh stucco I would give it as much time as possible both for curing and for settling and shrinkage cracks to develop (so you could have them repaired as part of the paint job)
3. If this is a contractor mistake, he most certainly needs to provide corrective measures.
4. You may want to ask him to fog coat the walls with acrylic fog. This may be a better solution for your situation.
5. If he suggests reapplying the color coat in the area where it was mixed wrong, your existing color coat must be removed first (this is typically done with sandblasting). Applying another color coat on top of existing will create two possible problems: A. Per bonding (i.e. you will be dealing with flaking before too long) and B. Stucco will be too thick at openings (doors and windows).
Best of luck!
Link to discussion on Houzz: