The word ominous refers to something that gives the impression that something bad or unpleasant is going to happen. There is a number of phrases or sentences which have a threatening ring about them. The first is:
It had come to be accepted that the pigs, who were manifestly cleverer than the other animals, should decide all questions of farm policy,...
The decision to give the pigs so much power turns out to be a huge mistake. They soon begin to abuse their authority and grant themselves privileges whilst the other animals were forced to make do with the little they had. This is clearly illustrated when the pigs, for example, claim the milk and windfall apples for their exclusive use. They also adjust the commandments to suit them, whilst denying the other animals similar privileges. The state of affairs degenerates to such an extent that the other animals are later worse off than they had been even in Jones's time.
This arrangement would have worked well enough if it had not been for the disputes between Snowball and Napoleon. These two disagreed at every point where disagreement was possible.
What makes this reference forbidding is the fact that the arguments between the two suggest that one of the two will either have to sacrifice or do something to ensure the success of the farm since constant argument and dispute would ruin its smooth running and, therefore, its success. In the end, it is the sly and malicious Napoleon who prevails. He manages to expel Snowball from the farm later by using the dogs he had removed and secretly raised.
... there were some violent debates.
The reference to violence has a sinister ring to it and predicts the terrible violence that Napoleon exerts on the general animal public once Snowball has been expelled. He has the animals slaughtered for opposing him and for secretly assisting Snowball during his secret visitations to the farm. In essence, he purges the farm of those who he believes are a threat, such as the four porkers who had complained about the Sunday Meetings being abolished. They confessed to having assisted Snowball and their throats were viciously torn out by Napoleon's dogs. Many other animals came forward to confess and were immediately slain. This violence unnerved and scared the animals and was a statement by Napoleon that he would not tolerate any challenge. His brutal savagery emphasized the tyranny he would employ.
... Napoleon was better at canvassing support for himself in between times. He was especially successful with the sheep.
This extract indicates Napoleon's secretive and pernicious nature and his wilful desire to dominate and manipulate. He would, throughout the novel, use the sheep to silence the other animals whenever they wanted to speak up. The sheep would, at appropriate occasions, bleat continuously, "Four legs good, two legs bad," which would be later changed to, "Four legs good, two legs better," when the pigs started walking on their hind legs.
Napoleon produced no schemes of his own, but said quietly that Snowball's would come to nothing, and seemed to be biding his time.
This is probably the most ominous of the quotes because it clearly illustrates Napoleon's intent. He seemed to be waiting for an opportunity to gain power and assert his authority. When this happens later, after Snowball's expulsion, Napoleon proves just how ruthless he is. He and the pigs disobey every single commandment and alter them to suit their purpose. Eventually, the pigs become even more ruthless than their erstwhile masters. They adopt human habits and start walking on their hind legs. In the end, the distinction between human and pig is completely blurred, so much so, that the animals could not say which was which.
Events on the farm had gone full circle. The animals were exactly where they had been before the Rebellion, with two major distinctions: they were much worse off and their oppressors were of their own kind.