One irony in the witches' statement lies in their own wickedness. These evil, wicked witches are predicting that "something" is approaching that will bring wickedness as if evil isn't already present in the witches themselves. That "something" turns out to be Macbeth, the first reminder that he has become wicked because of Duncan's murder. The major irony, which is a dramatic irony known to the Witches and to us but not to Macbeth, in this line is that immediately after the second witch says "something wicked" comes, Macbeth has his entrance.
As the apparitions conjured by the second witch appear one by one, Macbeth believes that the predictions are reassuring, yet he says he will kill Macduff to make sure that this enemy will not pose a threat. Then Macbeth is very interested to see the fourth apparition to determine if Banquo will have any descendants who will become king, as the witches had predicted for Banquo. Macbeth's horror at the show of eight kings followed by a bloody Banquo shows that he now believes Banquo's prophecy will come true. He will question why he has killed Duncan so that Banquo's children can be king. It appears that more killing will follow as Macbeth demonstrates just how wicked he can become.
Read the scene carefully beginning when the apparitions appear and the witches offer their interpretations. Macbeth's responses reveal his character.
There is irony in the fact that Macbeth was not aware of his own wickedness or the dark side of his nature until he met the witches and heard their prophecies. The witches themselves encourage his wickedness by feeding his ambition. Had they never arrived on the scene, Macbeth may have very well lived out his life in an honorable manner, whether or not he became the rightful King after Malcolm.
"By the pricking of my thumbs,/Something wicked this way comes" is ironic because the witches enjoy wreaking havoc in the lives of humans, take for example the witch toying with the sailor because his wife wouldn't share her chestnuts with the witch.
The witches are wicked to begin with and encourage this wickedness in Macbeth yet they ironically do the name-calling: "Something wicked...."