In the pre-title, 006(with the help of the general) fakes his death and then ends up angry at Bond for setting off explosives which injure his face. totally Illogical that he would be mad at 007for doing what he needs to do to escape at this point. He also kills a half a dozen Russian comrades while pretending to be a loyal Mi6 operative. Just messy. But the movie has it's charms no doubt.
If I may, I don't think this is a plot hole.
I think it likely that, after suffering such trauma as a severe facial injury, Alec wanted to apportion blame to someone - however irrationally - and considered the guy who set off the bomb as the most obvious candidate. I also suspect that he didn't like Bond in the first place. With the "for England, James?" tease, Alec is cynically mocking Bond's patriotism (an early hint, perhaps, that Alec and Bond don't quite share the same ideology). Later, he is obviously jealous that Natalya prefers Bond over him so perhaps that had happened several times before (I'm reading between the lines there, of course). On the train, when Alec rants off on him, he is clearly getting off his chest everything he has ever disliked about Bond - and everything he could not afford to say while pretending to be Bond's loyal colleague.
As for killing his Russian comrades: firstly, Alec is a bad guy who kills people. His plan would later take in the deaths of many others. He's out for himself. He's hardly going to get sentimental over the death of agents who, from way back, he was conditioned to believe were enemies. He might even genuinely hate Russians and be nonplussed about killing a bunch of them. More to the point, he's in deep cover. Killing their own agents is what those in deep cover do. It's the part they play. What would you suggest he do instead? Say he had forgotten to load up his machine gun? Suddenly become an appalling shot? That would be a bit suspicious, i would think.
But seriously, one of the conventions of spy fiction is that 'sleeper' agents always go that extra mile to convince. In one famous spy novel, for example, the traitor is the protagonist's wife. For another, there are a couple of times in 24 when Jack has to kill good guys to preserve his cover.
I hope that helps you enjoy the film more in future.
Edited by DavidJones, 16 February 2016 - 03:32 PM.