There is a pipeline monopoly!
"oil shipments via the trunk pipelines of state monopoly Transneft"

First, the Russian economy is littered with inefficiencies, ranging from a bureaucracy larger than the Soviet one, to incredible corruption at all levels, to a myriad of monopolies. Putin has not made it a priority to make things more efficient.

Second, there are many more likely causes. The actual thing that got Yukos was the accusation that it had not paid its taxes. Many, probably every Russian company and person, did not pay their full taxes at some time during the 90's. Not only was it selectively persecuted but the courts also froze all of the company's assets, effectively preventing it from paying off the taxes without selling off part of the company. There was definitely an ulterior motive. That motive could have been to block it from being bought out by Exxon (I believe?), or to create a huge Russian oil-block (under government control), or to remove someone who Putin saw as a political threat.

Whatever the motive, the persecution has succeeded in accomplishing all three of those, while not provably making the Russian oil sector any more efficient, which is why I doubt that was the cause.