I think everyone is struggling with the example itself, but let me suggest an answer to the underlying question: How can the lens be badly out of focus when the green dot indicates it is in focus while, for the same lens using live view as a focus technique, it is approximately in focus.

There are two possibilities that come to mind. One is that the lens is badly flawed in some fashion that is throwing off the Phase Detection AF system (causing it to mis-read the focus state), but still allowing it to form a reasonably acceptable image when actually in focus. That seems unlikely but I guess possible. The optics involved in PD focus do not rely so much on apparent focus as angle of incidence of an object's light on different sensors. At least conceivably some form of distortion might mislead PD sensors. Have not seen it, but can imagine it is possible. Maybe.

The other is that the lens/body combination has an extreme back or front focusing issue. Focus, on most DSLR's in optical view finder mode (not live view) depend on a very precise match between the optical path for the AF system and the sensor. Fractions of a millimeter can through this off badly, causing the AF system to think it is in perfect focus when the subsequent image is not. Many bodies permit this to be fine tuned, the D3300 does not so far as I know.

Focus with live view uses the main imaging sensor so there are no path length issues and no fine tune is ever needed.

To confirm that is the issue, you need a more continuous set of subject matter in the frame, so you can see not just that it is out of focus, but where it did focus. A simple way to try this photograph a pole or similar vertical item (even a person's legs) in tall grass, where you can see where on the grass before/behind it actually focuses. The trouble with your shot is NOTHING is in focus, apparently, so it is hard to tell if it missed focus before/behind, or was just blurred for some other reason.

If it is actually focusing in front/behind consistently, you are probably out of luck with that lens (lacking AF Fine Tune, the alternative is sending both together to Nikon, crossing your fingers they do not mess up the body for other lenses fixing it for that one -- but likely they would just say "not supported"). Even if it had fine tune, your example makes it appear too extreme to fix with it (emphasis on "fine" tune).

Or... you may find something wrong in your experimentation and examples. Such things are always best done multiple times, on a tripod, locked down, and repeated from scratch checking all the settings each time. It's VERY easy to let experimental error creep in (I know from making many mistakes testing lenses and focus and fine tune).

Update: As discussed in the comments below, even if your camera had AF Fine Tune (and it does not), it likely would be unable to apply that to a manual focus lens.