How to fix the focus on the camera?

I should know how to do this, having done photography since 2010 with D-SLRs, but I'm not yet accustomed to my newest lens which is a 50mm Nikkor lens. I use a Nikon D3100, so the auto-focus feature isn't available. I manually focus and I have done enough practice to understand that when a green light comes on in the corner, it's focused on part of the subject.

Well, last night it wouldn't work. That green light was flashing on and off and I looked it up. I fixed it, or so I thought. It doesn't flash on and off now and flashes when the viewfinder focuses; the picture would look sharp and exactly the way I'd want it.

Then I take the picture and it comes out blurry…

Added (1). I forgot to mention that for right now, I'm shooting on Auto. I shoot Manual, too, but for now I'm shooting on Auto.

Blurry. Is the shutter speed too long and you're getting motion blur?

You have solved your problem.

However, for clarity, "blur" is caused by camera or subject motion when you use shutter speeds longer than about 1/250th second

Shooting in "auto" has your camera trying to auto-focus an old NIkkor AF lens with NO internal auto-focus motor.

If you want to shoot in "auto", you will need to upgrade your lens to a Nikkor AF-S 50 mm lens

The reason the little green light (electronic rangefinder) is blinking is because you are not quite in focus and that will happen more when you are shooting in low lighting situations… If your camera has an auto-focus assist lamp, that will help when you eventually get your AF-S lens(es)

The answers you got are due to the comment you made that this happened "last night". This implies you are shooting in low light. The focus detection mechanism requires a certain amount of light to work. Since you are shooting an AF lens, you won't be able to use the focus illumination light. You should have gotten the AF-S lens which costs $100 more.

Shooting in Auto doesn't guarantee anything if you're not aware of the exposure settings your camera chooses. Low light situations is the time to shoot in manual, not auto. Since you didn't post an image, it's hard to say if you had a focus or camera/subject movement problem. In low light, the shutter speed may be very slow. If you didn't shoot using a high ISO, like 1600 or more, then motion issues will be apparent.

Look at the EXIF data of your images. The shutter speed will be listed. You can also set your camera up to show exposure settings when reviewing images. If you're shutter speed is slower than 1/30 seconds, you will end up with camera/subject motion issues unless you are well practiced in holding a camera still.

From experience, that light does not exactly stay on. It flashes momentarily when you hit focus then it goes off. If you really are concerned with sharp focus, use a tape measure. If you can get by with more DOF, adjust your aperture accordingly.

One last thing. Make sure you calibrate your camera's diopter if you haven't done so lately.