Why does this happen when using my Nikon camera?

I've found the aperture to do this strange thing. I adjust aperture it through the camera, and on some occasions, it can be adjusted to around f/3.5-ish and then sometimes it will only allow me to go down to f/5. I'm using a nikon D80 when I'm doing this. Any idea why I can't make it go down to f/3.5 all the time, when shooting in manual mode?

It is not the camera.

Your lens will change apertures when wide open when you move the zoom from 18 to 55 mm.

At 18 mm the widest f/stop is f/3.5, but when you zoom out to 55 mm, the f/stop becomes f/5.6

My guess is you did not read about this when you read the lens user manual

Your zoom lens has a variable maximum aperture that depends on the focal length chosen. At 18mm the maximum aperture is f/3.5. At 55mm the maximum aperture is f/5.It's normal. If you want, you can replace your kit lens with a constant maximum aperture lens. If you want better, buy a prime lens, one with f/1.8 or better yet, f/1.4!

What they said.

This is common on all consumer-grade zoom lenses.Pro lenses on the other hand do have constant apertures (i.e.f/2.8 throughout the entire focal length), which is one of the reasons they cost so much.