Depends on how interesting you want it to be.

a) While they're making an attack, some patriotic folks come in and fight back. These folks might be fishermen or they might be another set of smugglers. It might even be a warship that was out on maneuvers.

b) One of the ships in the harbor contains something dangerous. This might be a monster destined for a menagerie or simply tuns and tuns of flammable oil (which burns the ship quickly and maybe spreads on the water).

c) The dockside contains a shrine to one of the PCs deities. Fire on the docks is likely to burn the place down. You can substitute orphanages or convalescent homes for destitute hookers... whatever would motivate the PCs to be careful and creative.

d) Similar to b, something on the dockside is uniquely dangerous. A brewery (even just a small still can cause big problems)? A granary? Some wizard's iron golem? Remember, they don't have to fight the iron golem... they just have to avoid it, or even use it to their advantage.

Just a few options.