Well, first of all no one should be in prison for their politics. Political cases against people are just wrong. I wouldn't necessarily call this the first problem of the whole penal system, though.
The number one problem, in my view, is medicine. Or, rather, its absence. There is no medical care in Russian prison colonies, you just don’t get treatment. They give you the same pill for your head and for you're a**. In the Berezniki colony (where I spent my time after the sentence for my performance in the cathedral in Moscow), there was a tuberculosis hospital on the territory of the prison. That means that women with open tuberculosis were just a couple hundred meters away from everyone else in the prison. And since most women who are in prison (about 70-80%) are there because of possession or selling of drugs, this also means that many of them have HIV. These people have to be treated for HIV, and if they aren’t, their immune systems stops working and they simply die. The are constant problems with procuring HIV medication, if you look at the statistics it’s just terrifying.
More broadly, the whole Сriminal Code has to be reformed.
There’s also the problem of mandatory labour. What should a penal colony be for? Theoretically, it should prepare you for life after you leave the colony. Because isolation of being at the colony is already punishment enough. Our penal system is built around backward logic – the fact that you are there is not even considered to be the punishment.