In my opinion the biggest question or ambiguity in the play has to do with King Duncan's two sons. Does Macbeth plan to murder Malcolm and Donalbain on the same night he murders their father? If not, what can he hope to gain by killing Duncan? Malcolm is obviously the heir apparent to the Scottish throne. And the younger son Donalbain would become heir apparent if anything happened to Malcolm. The two sons are frightened when they learn their father has been assassinated. Both decide to flee for their lives. But Macbeth had no idea that this would happen. It gives him the opportunity to blame Duncan's death on Malcolm and Donalbain and enables him to become king.
There is a great deal of discussion and soul-searching before Macbeth kills the king. Macbeth argues about it with his wife and agonizes over the prospect of doing it in his soliloquies. But there is virtually no hint that any thought has been given to the big problem of what to do about the two sons. It seems evident that Shakespeare did not know how to handle the matter himself but left it to deal with after he had described what happened before, during, and after the murder of the king. Shakespeare knew he was a genius and felt confident that he could figure out a way to deal with Malcolm and Donalbain after he had written all his beautiful poetry about the plotting, the soul-searching, the murder, the discovery of the body, and everything else connected with the assassination. To deal with three murders on the same night was more than he could handle effectively on the stage. He hints that Macbeth and his wife had planned to kill the sons on the same night as their father but that several unforeseen events prevented it. One was that Macbeth imagined he heard a voice crying "Sleep no more! Macbeth hath murdered sleep," etc. Macbeth tells his wife the voice was loud enough to wake the entire castle. Then there was the prolonged knocking at the gate, which was sure to wake a lot of people up. There was also Macbeth's reaction to the one murder he had committed more or less against his will and conscience. When his wife tells him to take the daggers back to Duncan's chamber and smear blood on the grooms, he tells her:
I'll go no more.
I am afraid to think what I have done.
Look on't again I dare not.
Obviously Macbeth is in no condition to sneak into Malcolm's room and kill him the same way he killed the boy's father, and then go to Donalbain's room and do the same thing all over again. Besides, the boys may be awake! Macbeth seems ready to have a nervous breakdown--and yet the knocking finally forces him to go down to see why nobody is opening the gate. He has to conduct Macduff and Lennox to the very room where he knows the king to be lying on the bed covered with blood.
Finally, it would seem that Shakespeare gave some attention to the problem presented by Duncan's two heirs. He solved it by having them decide to flee for their lives, since they had no way of knowing how many men may have been planning a violent coup. Donalbain tells his brother:
Where we are,
There's daggers in men's smiles.
So Shakespeare does the best he can, although it leaves some unanswered questions. Why doesn't Malcolm stay and claim the throne as heir apparent? How does Macbeth manage to convince all the thanes, including Banquo, that the sons must have had their father murdered? How does Macbeth manage to get himself elected king so easily, especially when at least two of the thanes, Macduff and Banquo, must be pretty sure Macbeth was behind the murder? How does Macbeth justify killing the two grooms without giving them a chance to talk? Was it Macbeth's intention all along to kill the grooms when the body was discovered? It couldn't have been, because he didn't expect to be present. He wanted to pretend to have been sound asleep when the outcry arose. When Lady Macbeth appears in response to the alarm, she asks:
What's the business,
That such a hideous trumpet calls to parley
The sleepers of the house? Speak, speak!
She is doing what they both had planned to do--to appear in their nightgowns and pretend to have been sound asleep.