I have done the Stormcloak quests but still see legion soldiers with Stormcloak prisoners

Thats not the worst of it. You should visit Solitude and take a walk through the city.

Dont like the sound of that, havent been been to Solitude since but I am on my way now to do a burglery job.

If you explore in remote areas, you can still locate Imperial camps. Odd thing is though, some of the Legion soldiers are still classed as essential and can't be killed.

Basically, Bethesda svck at depth.

Ulfric didn't defeat the entire Imperial Legion if you 'win' for his side in the CW questline, firstly.

Secondly, after you 'win' for his side in the CW questline, talk to Ulfric and he'll talk about the remaining Imperials and what he expects of you

Thirdly, after I won for Ulfric in the CW questline, there were no more Imperial soldiers in Solitude. There were a couple banners still. That's it. If you go to the Blue palace and poke around, you'll find the displaced Jarls all in a cellar, complaining, and not liking you very much

The Legate in Imperial camps retain 'essential status' for some reason. It's an error. I assume that there was something they removed that involved the Legates, and they neglected to take away those NPCs essential status.

Complaints are fine but you can check most of this stuff out in the game. It's not Beth's fault you didn't talk to Ulfric afterwards, for instance

I didnt do the CW questline yet.. I may not.. Ever.

But what i believe is happening with tje essential flags is that you arent meant to completely erradicate the imperials. Most likely due for future history reasons. If you get my meaning.

They just arent meant to die. I could be wrong. But then again, i think im right. You did your duty. You overthrew the imperials. Now ulfic is free to reign. Thats it.