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If you meant that the focus is always a little bit off, that's normal. This is because that modern day DSLRs such as the Nikon D3000 has viewfinders that DOES NOT show the shallow depth of field a lens with a f/stop of lower than f/2.8 can show. This means that if you use your 50mm f/1.8 lens at it anything below f/2.8, the lens will actually show LESS depth of field than your viewfinder will show. This obviously creates problems as you never know which parts of the photos will actually be in focus when you shoot.

Another thing about lenses, especially wide-aperture primes such as the 50mm f/1.8, is that the image is always a bit softer and less contrasty at its widest aperture. The image quality improves as the f/stop value increase, and the best image quality is achieved at f/5.6 or f/8. If you're images are in focus but still appear soft, you can safely use f/2.8 without image quality concerns.

At f/1.8, your depth of field is very, very shallow. You have to make sure that you are focused precisely on the area you wish to be in focus. An example would be taking a picture of a person... if you focus on the tip of the nose instead of the eyes, most of the face will be out of focus.

The small, dark viewfinder of your camera doesn't make it any easier.

It takes practice more than anything, to get the shots you want. It may help to stop down a couple notches, if you can still get decent shutter speeds at f/4, your depth of field will not be quite so critical. Still important, but you will have a little but of breathing room.