Your question refers to what we call dramatic irony, which is when one or more characters and/or the audience know something that other characters on the stage do not. Of course, this concept is particularly relevant for this excellent comedy, because so much of the humour and the plot is built around the way that Viola disguises herself as a male, Cesario, who is in turn confused for her twin brother Sebastian, who she thinks perished in the shipwreck that threw her up on the coast of Illyria.
The specific situations where this is referred to are numerous, but one that we could analyse is when Olivia first meets Cesario, who is entrusted with the task of delivering his master's love to her. However, much to the audience's amusement, we see that Olivia, far from becoming enamoured of Orsino, has fallen in love with the messenger instead:
'What is your parentage?'
'Above my fortunes, yet my state is well:
I am a gentleman.' I'll be sworn thou art;
Thy tongue, thy face, thy limbs, actions and spirit,
Do give thee five-fold blazon: not too fast:
We as the audience know what Olivia unfortunately does not: that Cesario, the man who has charmed her so greatly, is in fact no man, but a woman disguised as a man. Our privileged position of seeing all the action gives us superior knowledge in this instance.