With these small copies of the pictures the first thing to strike me is how different the exposures are, visually, and of course the difference in auto ISO value is further confirmation. This is very likely due to the different composition including more or less of the sky - the very thing that auto exposure can get so wrong and which manual exposure can help you avoid. With skies like those the lighting is not going to be changing rapidly, if at all, and with manual exposure once you had it right it would stay right. Manual is how I'd be shooting in lighting like this.
As for the softness, it is hard to tell at this size, but as clear as day when viewing larger versions. With the subjects approaching directly towards the camera I don't think blur is the big issue here, although a little more shutter speed wouldn't hurt. I think the camera/lens has simply failed to keep up with the pace of movement with the subjects so close to the camera. Personally I'd be moving further back and using a longer focal length. Not only would I avoid a kick in the spheroids but I'd also reduce the relative closing speed of the subjects. Also, and this is very much a creative choice, by narrowing the angle of view I'd reduce the amount of background included within the scene and create a little more background blur.
On top of that, it does take a moment for the camera to get aligned to the pace of subject movement. I may be wrong, but I would guess that maybe you are not giving the camera sufficient time to lock on and track the motion. Ideally you would want to start focusing when they were at the rear of their swing and track them as they came towards you. Once their position was right in the frame you would then release the shutter.
This is all brilliant advice - except the shots were taken in Manual

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What the Interweb manual zealots forget to mention is that Manual is no longer Manual when you set Auto ISO:bonk:
The focussing advice is bang on, but it wouldn't have been much use to the OP, he was shooting AF S (which I think is Nikon for One Shot), so he wasn't tracking the movement.
As the focussing advice above is great, I'll elaborate (a bit) on why exposure modes are less important than the internet would have you believe.
It doesn't matter whether you shoot Green box, Manual, Aperture or Shutter priority or Program - If you don't take any notice of what your meter is measuring, you've no chance. Light meters are dumb, even clever ones. Just like with the focussing, they need telling what you want.
You've used multi segment metering, which is where the camera tries to evaluate the scene and come up with the right exposure. In those two pictures, one is exposed about right, the other one under exposed. The underexposed one has a larger proportion of the frame filled with sky, which has fooled the meter into thinking the overall light level is brighter, so the shot is underexposed.
If you'd shot Manual (without the auto ISO), and framed the picture exactly as the first one was framed to set your exposure - all of your shots would be as well exposed as that one.

Isn't Manual brilliant
But what if you'd have framed it for the 2nd shot and set your exposure? All of your shots been underexposed!

Why is Manual so stupid?:thumbsdown:
Of course the answer is to understand the scene you're metering. And then if you shoot Manual and the conditions don't change too much, you'll get consistent exposures. Of course - you could also use exposure lock on an auto mode and get consistent results too

and by re-metering the scene and locking exposure, you'd deal with changes in light levels as they occur - of course re-metering in Manual works the same.
The important issue isn't the exposure mode - it's understanding your meter. I hope that helps.