Reading between the lines, the problems are due to the break-up of the Soviet Union.

The launch base and consequent orbital paths for Soyuz were based on a rather larger Soviet Union. Russia has retained launch rights from its cosmodrome in Kazakhstan, but landing rights are perhaps more circumspect and one would certainly not want to stray from one friendly republic to another less friendly one.

Once the "commit" to de-orbit is made, the craft has a very limited endurance. perhaps not enough to make a complete extra orbit. Various support packages are jetissoned and tanks bled. If the crew are slow, or something on the ground delays them, they get closer and closer to that dreaded international border. If they fire the retros late, they must fire hard, and enter a steeper trajectory in order to get down in the right republic.

(all this is my own W.A.G., but it feels right)

At the same time, I suspect that the Russian space organisation has inherited a lot of the inertia, bureaucracy, and inefficiency of the Soviet era, despite efforts to the contrary. (Brilliant design cannot entirely compensate for politically-connected sons-of commisars or sons-of-farmers working the important consoles or having to give their approval for key mission steps)

So, I think the issues are about Soviet organisation - the whole apparatus was never designed for pin-point landings, but geopolitics has forced that onto the Russians.