Some possible reasons:
- Intense environment (ex: The beach... especially bad if you change the lens on site)
- Poor storage (dusty bag)
- My Favorite : Zoom/Focus pump effect ! Even if it is sealed, a lens is not "a partial vacuum" ! The volume is changing, thus there is air going in and out !
For example : A lens like this old push-pull Canon Zoom can be "weather-resistant", but with such a MASSIVE push-pull displacement, there is a lot of air entering IN the lens.
The newer version of this lens can stay cleaner, because many more moving parts are staying in the body. At the other extreme, a typical 70-200 2.8 Zoom like this one will not move externally at all, and thus stay cleaner.
Most lenses will at least vary on volume with focus (even primes), thus having a problem with what is in the air around them.
The lesson here: Don't play with your zoom in the sauna !