"It" here refers to the statement, "Whoever causes one of these little ones to sin".
What are you thinking the pronoun should be? Perhaps you think "he", referring back to "whoever"? But it is not "whoever" that the alternative would be better than. Jesus is not saying that being thrown into the sea is better than the person. He is saying that being thrown into the sea would be better than the action of causing little ones to sin. And an action is an "it". And there is only one action under discussion, so it is singular.
Just by the way, people who translate the Bible usually have a great deal of respect for the text, so they are very careful to have correct spelling and grammar. I'd be very cautious about supposing that there is a grammar error in a Bible translation. Well, except for non-standard grammar that is there for a specific reason, to convey a concept that is difficult to express with standard grammar. Like, "Before Abraham was, I am." The tenses are not correct in any language, but it's the only way to express the timelessness of God. The same kind of problem you might run into writing a time travel story. (Like I'm suddenly reminded of a movie I saw once where a character tells a time traveller where he's from and then asks, "Have you ever been there?" And the time traveller replies, "Yes, but not yet.")