Hey...
I don't seem to get any random thalmor or imperials moving around prisoners. I decided to check the Embassy, and there were about 10 Thalmor justiciars, just standing there at the gate.
Any way to fix this? I killed them all, still haven't seen any others patrolling.

I have seen only 3 Thalmor Patrols in the game, they are quite rare. Only once did they have a prisoner. I have never seen the Imperial's moving prisoners, but I have seen their patrols too, and they are just as rare.

Are you walking to places or fast traveling? I have only seen these patrols when I have walked through several outdoor cells.

I've only seen one patrol once (close to the western most edge of the map north of Markarth, south of Solitude) with a note on one of the guards saying that I was dangerous and needed to be dealth with on site! =]

Guess I pissed someone off earlier (perhaps when I delivered that Whiterun guy from the Thalmor fort)

I'm walking a lot now, but when I have to be at the other side of the world I just fast travel

I now late in the game have started to encounter Imperials with Stormcloak prisoners on a frequent basis. Even though I sided with the Imperials I release the Stormcloak and kill the Imperial guards for talking down on me after all I've done for them. No respect.

I generally try to avoid "killing them all" when I find something out of place. I've seen Thalmor appear on the roads in threes, sometimes escorting a Stormcloak prisoner, sometimes not. I've seen them attack me outright due to an Execution Writ in their possession, yet the next group I saw did not attack me. I've never seen a group of them outside the embassy, but I suspect that is due to me not advancing a particular quest. It is possible that once you progress to a certain point in a main quest that it is no longer appropriate for them to be wandering around.