Well that's one huge scene

It's difficult to isolate what's going on, without the objects being grouped at least. I hid most of the emitting surfaces, trucks, bushes, ground...and I still got the black dots until I hid the two objects:
Sign Wall Flood 1
Sing Wall 2 Emitters
But it's not certain these are the only ones causing the problem. Perhaps just having any emitter in the scene. You can try hiding all emitters and just render with skydome with sun on to see if you still get those black dots. If not, then try unhiding any emitter and check. A few things about the scene:
Material "App Bay Emitters assigned to just one tiny object" - hide or delete this one, may cause problems and add to render time
Displacement applied to some objects that may not need it (C_O_E_LDark)
Bump set too high on some materials (Daisy_Stem, Daisy_Leaf....) It's set to 200, you will most likely not get a higher bump with this value, just artifacts.
Many or all the emitters have much too high value, even when split up between different emitter surfaces. If you calculate their lumens it's over one million. It's better instead to work with real emitter values and adjust the camera parameters instead to get the right lighting. If you have these exaggerated emitter values some strange things may happen like these black dots.
"Lscape Emitter 2" objects, penetrating ground and too strong emitter values
"Red_Back_Light", not sure where this object is placed, looks like inside a wall.
Do you really need displacement on the flag? Maybe better to just model some ripples.
Also you have about 20 multi light sliders in this scene when ML is on and this is already a pretty heavy scene. Maybe you don't really need some of them, or merge some objects so you get less sliders.
I think it's easier for you in your modeling application to hide, unhide some objects, try and make it as simple as possible to make those black dots appear. Sorry I can't spend more time on it now, it's pretty difficult checking it from Studio.
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