I personally have not done this, but I have a friend with a couple of bikes and he's shared his challenges.
It sounds like you are breaking through the coating in spots, and they might appear in those spots as a side effect of the manufacturing process -- just a guess. I'm certainly not saying there's a defect, because they'll probably tell you to not polish it. I'm only saying that its becoming visible now that you're polishing it.
You can check with the manufacturer of the windshield, but you'll probably find most, if not all, are coated to protect from UV and provide impact resistance from road debris. You'll also probably find out that you're not supposed to polish it.
But as you probably have experienced, much like headlights, at some point that coating gets compromised enough to where you need to try polishing it to restore clarity, because replacement can be very expensive.
Removing deep scratches and pitting will likely require removal of the coating.
At this point you probably can't make it much worse.
One challenge with polishing motorcycle windshields, windscreens, and other similar pieces is their size, and getting an even polish that is visually clear can be difficult. And it's more obvious to you because of how the windshield appears in your line of sight. And if you've got the blotchiness of the coating having been removed in some spots, it can be more of a distraction.
Working in an even pattern with a polisher can be difficult over such a large area, but if you're working by hand now, give the polisher a try.
I would avoid wetsanding, but if you do, start with the finest grit that will do the job -- 1000 or 1200. I'd certainly avoid anything below 1000 without trying something above it first. Finish with 1500-grit or higher before polishing.
Keep in mind that the material may a little different than headlights, so the process can be a little bit more delicate.
If possible, experiment in an out-of-the-way area.
