These ideas were all originally conceived in or around the Capital Region, NY, but could easily be transplanted.
1) The Siege
A nearby sanctuary - holy ground, accorded neutral ground, whatever, a place where it's considered neutral and with a strong enough set of protections to enforce it - is cut off. Nothing seems able to get in or out. Is it a protective response to some attack from whoever maintains it? Is it an accident - a new ward going up that unintentionally backfired? Or is this an attack by someone external, an attempt to weaken the sanctuary far enough to breach it?
2) A Bridge over Quiet Waters
Water tends to ground out magical energy; therefore, rivers should disrupt ley-lines, right? Okay, your city's on the west bank of a river (Albany, Hudson), disjointed from the east-bank cities (Troy). A group, which already has strong influence over the east-bank ley-lines or magical energies, is trying to create a major ritual to bridge the gap - to extend their influence directly over the west-bank ley-line junction. This manifests as earthquakes, "magic-quakes", shifting ley-lines, and disruptions in the veil to the Nevernever. The group must attempt to stop them before they succeed, and increase their power by an order of magnitude.
3) The Faeries are Coming!
The Faeries are everywhere! Pixies invading gardens, goblins and ogres and trolls in dark alleys where they've never been before, elves and full Fae are displaced and homeless - and an all-out turf war seems imminent. Some investigation reveals that the nearest Faerie stronghold seems to have emptied out and then closed its borders - and none of the Fae are talking. Who took it over, or what are they afraid of? Is it an invasion by other Fae? A terrible monster? A magical experiment gone bad?
4) The Black Hole of Rensselaer
Engineers have always caused trouble - and a cabal of Wizards convinced Magic and Technology can mix, when they aren't being laughed at, can cause more trouble than most. The group notices a drop in magical energies in the region; investigation eventually leads them to realize that it's being drained into one location... Which happens to be the basement of a building at a local university. Is it an invention gone horribly wrong? A misguided attempt at helping the local mortals? An all-out attack on the local Fae population? The must fun, of course, is "D - all of the above"... As different members of the group behind it have different motivations. Can the group disrupt whatever device or ritual is causing this before the loss is permanent?
5) Muddy Waters
The river-monsters are restless - but is it their fault? Increased attacks, migrations, and the magical community is up in arms. But investigation shows that they're being disturbed out of their deep homes by pollutants - which suddenly are smogging up the mana in the water as well as being poisonous. Has some nearby industry accidentally caused this, or is it an attempt to drive out the river's inhabitants? What could be in the depths that would inspire someone to try this?
6) A Small Engineering Problem
The dwarves used to have it made - the biggest locomotive works in the country, orders pouring in! Then, General Electric - generators, all sorts of good stuff. Their skills went to good use. But their income has dropped to almost nothing - they've been cut out of the business, dumped on the wayside... And they want the good life back. Riots are the least of the group's problems when the union's made up of some of the most skilled tunnelers and builders in the world... And they're out for revenge on the region they see as having deserted them.
7) Old, but Still Got It!
Ol' Mame Faye ran a bordello for decades before she "died"... But recent sightings have made some people wonder if she's still around, 70 years later. At the same time, a new serial killer is on the loose - who seems to love people to death, leaving them in an agonized pose of pure pleasure. And the local graveyards are working overtime - spirits rising, sightings at night, and it not even near Halloween. Is it the White Court, finally moving in? Is it a necromancer, playing games with the dead? Is Ol' Mame Faye still around, either a wizard or a vampire, or is it her ghost roaming the streets? Are all these problems linked, or is the timing just enough to drive your heroes crazy?