Troubleshooting with Nikon D3000?

I'm a beginner in photography and am having trouble shooting. My pictures won't take, and I don't know what's wrong. My camera will focus but will not shoot. Depending on what I'm shooting, they will take. It seems that it will shoot darker areas rather well-lit areas, like near a window. It says to use a flash, but I turn on the flash and they still will not take. What's wrong?

If the cam can't focus it won't shoot the pic or if you have the remote option turned on. If that is on the button on the cam will only focus. Other than that its a internal error. Also a dirty cam and lens will cause identical problems.