The sons are afraid that they will get the blame for the murder of their father so Malcom flees to England and Donalbain flees to Ireland. The fact that they flee makes it more suspicious that they are guilty. The only people that know about what the Witches said are Macbeth, Banquo and Lady Macbeth, therefore no one else suspects them to be guilty. None of these murders would have happened if the witches wouldn’t have started messing around the fate of others. Yes, Lady Macbeth is the one who talked Macbeth into this. Yes, Macbeth id the one who actually does the murdering. Yes, the brothers did flee which makes them look guilty, but none of these actions would have happened if the witches would have kept to themselves.
The witches are the ones to blame when it comes to how and why King Duncan got murdered. If the witches had not told Macbeth and Lady Macbeth of his possible kingsmanship then Macbeth and Lady Macbeth would not have gone crazy trying to make that rumor true. It all comes down to our own perspective but I think I have proven a pretty good point about why I believe the witches are in