Out of universe explanation :
The film is about the Suicide squad and Batman or the Flash barging in to save the day wouldn't make much sense as 'Dr R Dizzle' pointed out.
In universe explanation :
This mission was about proving the worth of Waller's Suicide squad to the elites. Batman saving the day would have just been an embarrassment for her and she might have asked Wayne to stand down until they were sure of the squad's failure if he wanted the files.
That would mean more casualties in case of failure but that wouldn't be out of character for Amanda.
We don't know about the Flash but we can safely assume Amanda Waller has leverage on him (as well as everyone else :
Because getting people to act against their own self-interest for the national security of the United States is what [she does] for a living