As a frequent traveler to LIM I have noticed the smells too.

One of them is the sea; the ocean there seems to emit a strong fish/salt smell. This is usually only an issue when I am in Miraflores or Callao.

The second smell I notice I've always attributed to the plumbing and the fact that you are not supposed to flush the toilet paper because the pipes are so old and fragile. Thats why the bathroom stalls always have those little trashcans next to the toilets.