Why are Malcolm and Donalbain suspects in the murder of their father? What motive is attributed to them? Why is this accusation ironic?

The accusation that Malcolm and Donalbain were responsible for the murder of their father is ironic because they fled for their lives and were accused of fleeing because they were afraid of being charged with the murder. The main accuser is undoubtedly Macbeth, who wants to be elected king to replace Duncan. He has a lot of clout because he is a great hero, loved by Duncan, and is both Thane of Glamis and Thane of Cawdor. The two sons become suspects because Macbeth seizes on their flight for their lives as a golden opportunity to dispose of both of them, and especially Malcolm, as having priority over him in the line of succession. Malcolm probably should have stayed and claimed the throne. His father had already publically proclaimed this in Act I, Scene 4.

Sons, kinsmen, thanes,
And you whose places are the nearest, know
We will establish our estate upon
Our eldest, Malcolm, whom we name hereafter
The Prince of Cumberland; 

And Macbeth says to himself in an aside:

The Prince of Cumberland! That is a step
On which I must fall down, or else o'erleap,
For in my way it lies. Stars, hide your fires;
Let not light see my black and deep desires:
The eye wink at the hand; yet let that be
Which the eye fears, when it is done, to see.

As heir apparent, Malcolm should become king upon his father's death. Shakespeare never makes it clear whether Macbeth had intended to kill the two sons on the same night he killed their father. If so, Macbeth was thwarted by his own loss of nerve, by imaginary cries of "Sleep no more, Macbeth doth murder sleep," etc., and then by a loud and prolonged knocking at the gate. But Macbeth is in luck. He had no way of foreseeing that Malcolm and Donalbain would flee. Both boys are young and scared. To be suddenly fatherless is terrifying. They don't know how many thanes may be plotting against them. They flee for their lives, giving Macbeth an opportunity to blame their father's murder on their conspiracy. Their motive would have been for Malcolm to claim the throne and then to give his younger brother all sorts of honors and emoluments as a reward for helping him.

Shakespeare had a big problem with Malcolm and Donalbain. He didn't want to stage a triple murder in three different rooms in the castle, and he didn't want to make his hero Macbeth look any worse than he would look for killing the kind old King Duncan. Shakespeare probably decided to deal with the one murder and all the consequent emotions experienced by Lord and Lady Macbeth, and then think about what to do about Malcolm and Donalbain later. Shakespeare was a great genius, and he must have known that he could think of something when the time came. His solution to the succession problem was to write a little scene in which both boys decide their lives are in extreme peril and that they should get away as quickly as possible. In their absence, Macbeth can accuse them of anything and displace Malcolm just Claudius displaced Hamlet while he was absent at Wittenberg.

Shakespeare seems to be placing the Malcolm-Donalbain problem on the back burner, so to speak, when he has Macbeth say to himself:

Stars, hide your fires;
Let not light see my black and deep desires:
The eye wink at the hand; yet let that be
Which the eye fears, when it is done, to see.

This is highly ambiguous. It might be interpreted to mean that Shakespeare intends to have Macbeth do something but he doesn't know exactly what. The playwright just couldn't see how he could have Macbeth kill three people in one night. Less is more. The murder of Duncan is more effective without adding the murders of Malcolm and Donalbain either onstage or offstage. 

In Act II, Scene 1, Macbeth seems to be sounding Banquo out about helping him dispose of Duncan, Malcolm, and Donalbain.

BANQUO: All's well.
I dreamt last night of the three weird sisters:
To you they have show'd some truth.

MACBETH: I think not of them:
Yet, when we can entreat an hour to serve,
We would spend it in some words upon that business,
If you would grant the time.

BANQUO: At your kind'st leisure.

MACBETH: If you shall cleave to my consent, when ’tis,
It shall make honor for you.

BANQUO: So I lose none
In seeking to augment it, but still keep
My bosom franchised and allegiance clear,
I shall be counsell'd.

MACBETH: Good repose the while.

With Banquo's help, Macbeth could kill the King and both sons easily, but Banquo knows what he is driving at and turns him down flat. Macbeth has to go it alone and only succeeds in killing Duncan, whether or not he had planned to go on and kill Duncan's two sons.