In any volatile situation, problems will develop that cannot simply be explained away. Napoleon is interested in his own gain. As an opportunist, who makes no real contribution to the struggle and only furthers his own need for power, he needs to be able to dispel fears and rumors and create so-called 'peace' through fear and manipulation.
Napoleon recognizes Snowball's superior intelligence, which is why Snowball is such a threat to his leadership. Once he has got rid of Snowball, he can use him as a scapegoat and establish him as 'the enemy' - not only Napoleon's but the farm's enemy. Snowball is not there to explain himself or refute Napoleon's claims so
he can blame every setback -- many of which are due to the failures of his own ideas -- on Snowball.
The animals are so afraid, having seen the results of disagreeing with Napoleon, upon the death of their friends - "the traitors"- so they would not dare contradict him.
To ensure that there is not a revolt and that there is no-one strong enough to lead a revolt, Napoleon uses Squealer to convince the animals that there are forces acting against the better good. Napoleon excuses his own ascendancy to being in the interests of the farm and to stop the animals from making "wrong decisions."
Napoleon confuses the animals with talk of "enemies of the farm" being Frederick and then Pilkington. The animals hear only snippets of information, enough to make them more confused. Obviously Napoleon must be the best person for the job as he is clearly not confused ! They do not really believe this but they do not even trust their own recollections, especially when the Commandments are constantly changing.
Ultimately, the Commandments become unimportant and have been
erased from the barn wall and replaced with a single Commandment: "All animals are equal, but some animals are more equal than others."
The animals confusion compounds the problem and the animals ability to recognize Napoleon as the enemy is non-existent.