So I did a side quest involving going to jail in Markarth, and participated in a riot (I am trying to include necessary information without any spoilers) killing guards. After the riot was over, I had a bounty on my head in the Reach (which I just paid off), but whenever I enter the city I am stopped.
When I choose to "go to jail", the guards pause for a second and nothing happens. They stop me again seconds later and that dialogue option is no longer available, and I am only presented with the option of fighting them. My guess is that, because I did the quest and killed guards (wouldn't recommend it), which involved me going to jail, the game is reading it as already completed, therefore not allowing me to get rid of said bounty. This is prohibiting me from doing anything in or around Markarth.

If anyone has any advice regarding how to get rid of or around this issue, information would be well appreciated.

Nevermind, I found a potential solution (quoted DISHTY on a Gamefaqs forum):

"If you have the problem of the looping dialogue with the guards in Markarth (as I did), then listen up!

Now, with any luck you have NOT started the civil war quest line, otherwise I am sorry, this is not gonna work, also I dunno if this will be manageable on consoles.

Anyway, join the Stormcloak rebellion and go through the quests on there. At some point after taking Whiterun you will move on to liberating The Reach. This quest line will involve you going to Markarth to bribe a guy in the keep which is where console players will have a problem.

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FOR CONSOLE PLAYERS:
When you need to bribe the guy, I guess, if you can, fast travel to Markarth Keep and sprint through to the guy's room (to the right of the Jarl's throne), steal the thing from his dresser and talk to him as quickly as possible. You will get stopped by the guards but you MAY be able to get through without them wanting to kill you.

To do this you will need to skip through the dialogue with the guards, selecting to go to prison every time, then as you will know, the dialogue will loop. When it comes up with "What's the matter" (something like that), at this point, exit out of the conversation and run in the direction you need to go, you will have to keep doing this, probably getting stopped by guards several times along the way (it may not even be possible).

Basically, you need to get to that guy without having all the guards trying to kill you as 1) the guy won't speak to you and 2) the guards will kill you during your conversation. Good luck with that!

FOR PC PLAYERS:
This is how I managed to do the quest when you bribe the guy. Quite simply, fast travel to Markarth, but before doing so, type "tcai" into the console.

(To bring up the console press the tilde key (~) on your keyboard (to the left of 1 and under Esc). Simply type "tcai" (toggle combat AI) and press enter, then exit out by pressing the tilde key again. This will make sure that no one attacks you, so feel free to waltz through the guards, steal the guy's thing (amulet I think) and bribe him.

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Now that you have completed that quest, do the next 2 quests (killing a troop of guards, and taking over a fort) and then you would have liberated The Reach. Now, with any luck, your bounty should have been removed - it was for me. The reason for this is that the Stormcloaks now rule Markarth and the Imperials can now be found in the Blue Palace. Any quests you needed to hand in to the guys in Markarth Keep can now be found in the Blue Palace (near Solitude)."