There seems to already be something in-built to the setting creation and issues that would cover your ... issue.
There are two kinds of issues: Current Issues, that are defined as you say. Impending issues however, seem to cover exactly what you are asking.
Fate Core p.22
Impending Issues: These are things that have begun to rear their ugly
heads, and threaten to make the world worse if they come to pass or
achieve a goal. Protagonists tackling these issues are trying to keep
the world from slipping into chaos or destruction. Examples: an
invasion from a neighboring country, the sudden rising of a zombie
horde, the imposition of martial law.
Decay and Corruption and
Conflicting Identities are both less tangible aspects, but they affect the city and the feel in a real way, and if not taken care of, can become more current issues and threats.
To give examples of what I mean in more tangible terms (and at this point I have to make assumptions as to what these mean- this is the sort of thing that should be hashed out in setting creation).
If by Decay and Corruption we refer to the government infrastructure, the seeps into every interaction they have with the powers that be, whether it is the corrupt Police Department, Government Bureaucracy, etc. If refer to the city itself, it comes into focus in the settings and places where the players find themselves being decrepit and dangerous or there being other examples that show up even in the news and such with fires, etc, creating a generally dangerous situation where morale is low in the city. There are several examples of such in the US that we see every day where the decay and corruption is endemic, and it is definitely a wider problem to be fought by the players than can be distilled into a single encounter.
Moving on to
Conflicting Identities, I will use the more obvious interpretation of the 'wrong side of the tracks' and the 'haves and have nots'. As time goes on and the tension rachets up between the two sides, it will definitely have a feel of impending movement towards being on the front burner. Otherwise safe areas of the city becoming less so because of the conflict between the two sides, and more ordinance put in place to keep things under control.
These are very useable aspects in many cases in the every day conflicts the PCs face, from a building collapsing around them, to the functionary that gets in their way (or helps them for cash), etc.
In another question, we talked about hidden aspects being useless as they don't engage the rules. The same for aspects that have no real narrative meat to them. If they are not going to engage the GM's/Players' narration, then they really aren't aspects- but something that is included in a blurb about the setting. And that brings us to the reason not to turn a theme into an aspect- if it has no narrative use. Just as when creating aspects for a character, you look for things that can be used positively and negatively, and is evocative, the same would apply in this case. If it doesn't pass that muster, then there's really no need to make it into an aspect.
Other Notes and Uses
One last thing to remember- there are less obvious uses for situational aspects that are not tapped into very often, but can be very powerful narratively. The players are not just moving through the background, they are also a part of it. If the city is
Decaying and Corrupt, then how does this affect the PCs themselves? What about the
Conflicting Identities... how does this affect them? What side of the conflict do they identify with? What part of the city do they live in, and where did they come from? How does the corruption affect their mindview?
To show this, compel the aspects not just against the environment- but against the PCs themselves. Get them involved in the narrative of the city itself... and invoke the role-playing aspect in the narrative. "You've subdued the gangbanger, and should turn him over to the approaching cops. But as you look into his eyes, you realize that could have been you. You work on the side of the angels now... but your past calls to you to give him a chance." slide a fate point to him, compelling conflicted identities. "What do you do?"