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.

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