Why was Uldren Sov in the Prison of Elders?

Uldren Sov was indeed imprisoned there.

Following the events of The Taken King, everyone thought both Uldren and Mara Sov were dead. However, Uldren somehow survived, and ended up shipwrecked on Mars.

The sound of her voice ripped him from sleep. He jumped up; his ship was still contained in its protective sphere. He tried to retract the shield, but it was locked to its initiation time. He couldn’t remember activating it. Then he remembered the battle. That blast.

(...)

He climbed out and saw the damage to his ship, and the truths of the armada's devastation sunk in.

He turned in despair to find hundreds of his Crow drones, deployed on Mars long ago, circling his ship, waiting.

“Welcome back, Master.” The one closest to him spoke first, and the others followed, a wave of salutations echoed throughout the dry sea.

And with that hope returned.

“Begin repairs on the ship immediately. Something has gone missing and you will help me find it.”

There are hints he might have an affliction of some kind, after he survived the blast at the Battle of Saturn.

There is something in his eye. He blinks and blinks, trying to rub it away, and as he does, he struggles to hear her, to sense that prickle of starlight under his skin. She will tell him he is on the right path. She will tell him she's still alive.

He feels nothing.

Uldren spent some time with his allies from the House of Kings. At some point in time, he confronts Illyn, as described in the lore entry Free | Part I:

"Admit it! Admit that you trapped my sister in the Dreaming City!"

(...)

That evening, he surrenders himself to the Reef.

In the next entry, Free | Part II;

They take him to a discreet landing dock on one of the lower levels of the Prison of Elders. When his containment unit hisses open, the glow and the mist silhouette an Exo with glowing blue eyes and a woman with her weapon drawn. Petra herself.

Petra Venj makes sure that only those three - Cayde-6, Petra, and Variks, know that Uldren Sov is in the Prison of Elders:

"I know. It's… Something's wrong with him, Variks. He's… mad. Lock him down—lock down the entire cellblock. No one in but you or me. Speak of this to no one. As far as the system is concerned, Uldren Sov died over Saturn."

Variks, who is the warden of The Prison of Elders, does not know where his loyalty truly lies. After a while, he shows that his loyalty lies with Uldren, opens all cells in the prison, and escapes through the same secret passage that they used to smuggle Uldren through undetected while the prison is in chaos.

Uldren escapes, and continues his campaign to free his sister, which he believes is still alive.

The history of the Reef starts in Destiny, and progresses through The Taken King, and the rise of Oryx. In this expansion Oryx destroys the Awoken fleet in the Reef, and presumably kills Mara Sov, but we see Uldren Sov escape the blast.

Destiny | The Taken King | Introduction cinematic

However, it can also be assumed that

Uldren Sov is still on Mars

and

If you stand near Executor Hideo, there is a random voice line you can hear from one of the unnamed npcs talking about how he knows his sister is alive at the reef and he wants the guardian to go find her

Referenced in this post.

If you inspect Telesto, it's flavour text is

Vestiges of the Queen's Harbingers yet linger among Saturn's moons.

So this could be taken as some of the Awoken loyal to the Queen did escape Oryx and Ghaul.

It's worth noting that The Reef wasn't destroyed by Ghaul and the Red Legion during the Red War campaign either, but we're not told about this in the campaign of Destiny 2.

Some NPC's in Destiny 2 talk about being able to reach The Reef, so presumably since the Queen's absent, Guardians are not welcome in The Reef any more.

My take on it, having played only the first Forsaken mission.

To me this makes sense. As Uldren Sov will blame the Guardians for drawing Oryx to the system after the death of his son Crota, and causing the destruction of the Awoken fleet. With his sister out of the way, he's free to claim ownership of The Reef. I think he breaks the barons out of the Prison of Elders to build his army.

The Vanguard also state to you that they will not go to war with Uldren Sov, and if you do, you are on your own.

So to answer the question, I don't believe that he was. I think he went in to break out the barons.

Ninja edit
I found some more reference material for those who like reading.

• The Maraid - The reef wars
• Mara Sov
• Uldren Sov