There are two reasons why the second witch says
'By the pricking of my thumbs
Something wicked this way comes'.
The first reason is since they last saw him, Macbeth has committed two evil murders: Duncan's and Banquo's. At least before the first Macbeth hesitated fully aware of how wrong it was. There was no such hesitation before the second, which also intended to 'take care of' the child, Fleance. This suggests that Macbeth has indeed become evil.
The second reason why the witch says this, is to do with the delight they feel: it is they who have brought out the evil in Macbeth!
This delight is suggested by the happy rhyming couplet and the 'pricking' or tingling of her thumbs, such a tingling sensation normally indicating pleasure.