I think the Ukraine government is stuck in a difficult position. I believe they want to leave some military forces in Crimea as their last toe-hold on the territory, but they have no means to support them. Being politicians, they don't want to be criticized for telling the troops to surrender their bases and come home. Nor, do they want to be held accountable for telling the troops to stand fast in their postions and possibly see something bad happen to them. Therefore, they just won't provide any direction at all, so that they won't be held accountable for any bad decisions. Therefore, those unfortunate troops are left on their own.
I doubt that there's much the Ukraine military can do in this situation. The Russians are simply way to powerful to oppose in any meaningful way. I'm sorry to say that NATO won't go to war over Crimea. There's no way that it could be confined to that region. If Russia were to invade the rest of Ukraine, well, all bets are off.