What is the meaning of the idiom 'to have a word with someone'?

The usual implied meaning is that the "someone" that you're going to "have a Word with" has done something that you take issue with. Saying you're going to have a Word with them means you're going to talk to them -- often to chastise or threaten them, as the case may be.

This is similar to the idiomatic "have Words with", which means to have a discussion, or more commonly, to argue with someone.