They see it as "payback" for the EU/Nato's support for Kosovo's unilateral declaration of independence. Interestingly, Spain is probably the only Western nation that doesn't recognize Kosovo's independence.
Same reason they supported Brexit - it causes instability and weakens the EU.
If I had to guess: (1) Because they feel that it would add legitimacy to the "referendum" they held in Crimea, if only by comparison and (2) just generally to cause trouble in the EU.
Russia seems to like Europe destabilized, in all possible ways.