One of the first signs that the witches may not be serving a pleasant purpose is their entrance. they come in after the stage direction of "thunder and lightning", implying a supernatural nature and a darkness due to their entrance with the storm. Next, they each relate the mischief/evil they've been up to, including "killing swine" and planning to curse a sailor because his wife didn't offer them chestnuts. One is carrying a man's thumb around with her, which is not something that mortal, moral people usually do.
Finally, the witches clearly have premonitions. They know that Macbeth approaches without seeing him, & they "read" Macbeth and Banquo's futures. They are described as shrunken and withered, and Banquo remarks that they look like women, but have grown beards. All of these characteristics point to the supernatural, dark nature of the weird sisters.
The witches enter in the midst of 'thunder' as in the play's opening scene, the 'thunder' being incantatory. In the conversation that follows, we are made aware of the witches' preoccupations of mischief, apart from their vulgar pastimes like 'killing swine'. The First Witch ventilates with a lot of vile passion how she is going to cause harms to a sailor whose wife refused to give her chestnuts: ' I'll drain him dry as hay:/ Sleep shall neither night nor day/ Hang upon his pent-house lid;/....Though his bark cannot be lost,/ Yet it shall be tempest-tost'.
As the witches appear before Banquo and Macbeth, the former doubts their bonafides: 'So wither'd, and so wild in their attire,/ That look not like the inhabitants o' the earth'. They have strangely grotesque features like 'choppy finger', 'skinny lips' and beards. When the 'weird sisters' vanish, Banquo iterates their strangeness: ' The earth hath bubbles as the water has,/ And these are of them.....'
Thus a close look at the witches' appearance, their clothes, their gestures and language shows that they were instruments of evil/darkness.