Ok, after completing the Stormcloak quest line, and complete the final quest, "No One Escapes Cohna Mine".
You get a terrible bug that has hindered me from continuing various quest lines such as the Dark Brotherhood quest line and the Thieves Guild quest line.. along from the many other quest that are started within Markarth.
Every time a guard sees you, they'll run up to you and say, "You are under arrest for conspiracy against the jarl.. etc" (or something along the lines of that), and you get the options of saying, "Im with the guild etc.", "It wasn't me, I've been framed", "I submit, take me to jail", or "I'd rather die than go to prison". None of these options work either, if you decide to go to jail, it doesn't work, it just brings up the option, "What's the problem?", and if you decide to die rather then to go to prison, then they kill you, so it completely keeps you from doing any quest and talking to any other NPC's within Markarth.
I've seen this complained about many times, but it's still not been fixed, what the hell's up Bethesda? Get to work. Fix this damned glitch because I've put 92 hours into my one character, and I'm not up for starting another character at this moment.

I'm not sure if this is a glitch only towards one system, but I play on Xbox 360, so let's get another update out there for the Xbox 360. Otherwise, this glitch really kills the game for me, I love the overall design of Markarth, and i'd love to go back to it without getting a** f***ed by every guard there. I also really need to continue the Dark Brotherhood and Thieves Guild quest lines.

So if I were you Bethesda, I'd make fixing this a top priority.. Please and thank you <3

Here's how to fix it:

Make sure you have enough to cover your fine.

You then need to sneak back into The Shrine of Talos, kill the hostel guards, but leave the none hostel one ALONE!!

Run through the dialogue, letting them take you to jail.

You will appear in front of the jail with a clean bounty, and you can then carry on.

I got it to, and this is exactly what I did.

It's been said you can kill all the guards in Markarth first, then enter the shrine, but I preferred my way.

Thanks, I'll try it right now.