What grit did you sand with?

Is the sheen otherwise good?

Those swirls may have been from a heavy hand from a previous coat. Are they reducing with each subsequent coat? If yes, they will eventually disappear.

Alas, I think you've reached the point of graduation on the Waterlox education. You know all the things to do, and are trying to do them properly. From here, I believe it's a matter of touch and practice. I had similar issues when I was starting on Waterlox, but knowing how it feels and what to anticipate now, makes it like second nature. I find it now hard to 'mess up'. You will too if you keep at it.

To answer your previous question about rubbing in:

I like to flood on my first couple coats and rub them in to the absorby areas. I may stay for 10 minutes on a large table top this way on the first and second coat. This truly is a rub in. This only has value before the wood is sealed. After, your mindset should switch to polish when doing wipe on. If you try to rub in to the sealed surface, you're just going to overwork the surface and get swirls or streaks.

In fact, I like such a thin top coat most of the time, I wipe it on and then buff most of it off. Done this way, I am just looking for an evenly sheened, moist surface, not wet - not even slick.