Wow.... those are some nice macro shots of the flies !! I don't know what they are other than.... flies
Are you growing indoors or outdoors ? If outdoors, have you had a lot of rain lately ?
It looks like a fungus has found a home on the bottom of the leaves. Probably from the leaves being too wet for a period of time. That fungus can cause the damage you see.
As for the flies, maybe they just stopped by for a drink of water ? I really don't know. I don't see a lot of mechanical damage on the leaves. A fly that large should cause a lot of damage if it was feeding on the leaves. You could keep an eye out for the larvae though... maybe the flies are planting their own seed on your plants.
Just my thoughts,