This article is a bit misleading by only using a partial quote from the head of Roscosmos immediate after the "sparking rumors of sabotage" line. Here is the full quote from the TASS article:

"We are considering all the theories. The one about a meteorite impact has been rejected because the spaceship’s hull was evidently impacted from inside. However it is too early to say definitely what happened. But, it seems to be done by a faltering hand… it is a technological error by a specialist. It was done by a human hand - there are traces of a drill sliding along the surface. We don’t reject any theories," he said.

"It is a matter of honor for Energia Rocket and Space Corporation to find the one responsible for that, to find out whether it was an accidental defect or a deliberate spoilage and where it was done - either on Earth or in space. Now it is essential to see the reason, to learn the name of the one responsible for that. And we will find out, without fail," he pledged.

So they are not ruling out sabotage, but neither are they ruling out it simply being a "technological error" either in space or on the ground.

The Soyuz spacecraft will be used to return astronauts Sergey Prokopyev, Alexander Gerst, and Serena Auñón-Chancellor to Earth in eight days.

I forgot that they had to use this Soyuz to get home. Really glad the hole is not in the ascent/descent module of the Soyuz!