At the beginning, Koskov is questioning Bond about the sniper Bond disarmed (Kara). Only later in the film do we realize that he was trying to see if Kara had been eliminated to avoid revealing the truth about the "extraction".
Bond is also notably curt in cutting off Koskov's line of questioning, giving an answer that essentially lets Koskov draw his own conclusions ("I'd rather not talk about it."). Having clocked that the sniper wasn't a professional, he's got some early suspicions that all might not be as it seems with Koskov's defection.
Whitaker is said to be a failed student of West Point and a strategic moron, but within his mansion, there are a number of statues of generals... including Adolf Hitler, a man who made a number of utterly stupid decisions during World War II and was also a huge slacker, preferring to go on daily movie marathons instead of actually running Germany. If Whitaker thinks of him as a 'great general,' it only solidifies the idea that he was a terrible student of war.
Notably, Koskov, Whitaker and Necros are mostly immune to Bond Villain Stupidity - most of the obstacles to their plan that comes up are from elements they could not have foreseen:
Probably the single most unwise choice by Koskov is requesting Bond's involvement in his escape, simply because it leads Bond to be involved in investigating everything else about Koskov's plans. Even then, this has short-term benefits - it's clear Saunders is out of his depth with the operation, and it would have likely failed had Bond not been there.
Koskov successfully sold MI6 on the need to assassinate Pushkin, something that M makes clear when discussing the assignment with Bond. Pushkin only survives because Bond has a history with him, giving Bond more doubts about Koskov's story, and because Kara survived because of Bond's actions, she is able to tell him her side of the story, unravelling it even more.
Koskov's other big mistake is having Bond and Kara jailed in Afghanistan rather than killed, allowing Bond to promptly escape with Kara - but then, since he is maintaining his cover as a KGB general in good standing, it's actually less suspicious to have them thrown in jail to await trial for murder, rather than order them summarily killed.
Bond's characterization in this movie, burned out and apathetic, makes sense when you realize that this film takes place in 1987, and the year prior he had seen his best friend, Alec Trevelyan, murdered. Except not really.
Bond witnesses 004 being killed in a climbing accident - which is how his parents died. Except here, the "accident" is a very deliberate and cold-blooded murder by an enemy agent, cutting the rope.
