Crossover rules, mate. It wasn't Flash or Batman's movie. I know we don't like it, but it's the same imposed rules we see in comics and other movies. Why do no Avengers help Tony in IM 3 when his house was blown up by terrorists? Why do no Avengers help Steve when they learned SHIELD was infiltrated by HYDRA and planning mass death with the hellicarriers in DC? Why does Superman never just pop over to Gotham to stop whatever multi-issue crisis Batman and his family are having? Story is not about them, so they weren't included.
With the old rules in Marvel Comics, you would at least get a shout out of what other heroes were doing when shit was going down. Mainly because 99% of all of Marvel's heroes were in NYC (Spider-Man, Daredevil, the Heroes for Hire, Fantastic Four, Avengers, Doctor Strange etc).
Like I said, it was only a minor annoyance. And to clarify that more, the annoyance is not that it happened but how it happened. In every other case, I've always considered the 'but where are x?' argument to be completely ridiculous. Especially so in the Marvel movies, which have always had very obvious reasons why other characters would not be available, or would not be appropriate to involve, or simply would not be allowed to be involved (as is the case in IM3, where the perfectly in character arrogant as hell Tony is trying to prove something to himself, and therefore doesn't tell anyone where he is or what he's found).
The problem in SS is just that they spend a good ten minutes of the minute actively showing these two completely unrelated heroes (who we know can travel very easily) dealing with problems that are very similar to what's happening in this movie, they give not the slightest hint of an idea that there might be something else out there taking up these two characters' time, they make the villains' plan so big and obvious that it has to be on the national news telling them exactly where to go, and then explicitly state this has been going on for days before the Squad shows up. They just took it too big to really be credible anymore, and including those cameos of Batman and the Flash catching metahumans just feels like they were practically begging the audience to ask 'hey, why aren't those guys around?'
I haven't seen it, but I saw a summary of the scene, and it sounds more like it's setting up a future conflict between Bruce and Waller over the Squad's existence -- she keeps it around, Batman tries to shut it down, and there's your plot for the sequel. Maybe the next movie will be Batman v Suicide Squad: Mid-Afternoon of Villainy.
I'm sure that was the intent, but it just felt kind of weird. I believe the exact quote was 'Shut it down or my friends and I will do it for you.' Something like that, anyway. It's just that, coming at the end of the first movie of a brand new series featuring mostly new characters and seeing the most established and respected character in the franchise pop in and say 'you're finished!' feels very much like the opposite of James Gunn's "The Guardians of the Galaxy Will Return".