Macduff has been suspicious all along of Macbeth's role in the death of King Duncan. When Macduff does not attend the banquet dinner that the Macbeths give at the castle, Macbeth notices the conspicuous absence. He inquires where Macduff is and is told that Macduff went home to Fife. Macbeth is becoming more and more paranoid, and he goes to see the three witches again. The "weird sisters" warn him to "beware the thane of Fife."
Therefore, both Macduff's failure to attend the royal banquet and the warning given by the three witches are what causes Macbeth's displeasure with Macduff in Act III.
Macduff is in trouble with Macbeth because he has failed to appear to a political and social function to which Macbeth has invited him. Further, Macduff has acted strangely toward Macbeth ever since Macbeth was named Duncan's successor to the throne (after Duncan's death and Malcolm's flight). Though Macduff is a Scottish lord and therefore should have attended Macbeth's coronation at Scone, he chose, instead, to go home to Fife at the end of Act II, scene iv.
Now that he's ignored Macbeth's explicit invitation to his home, he has slighted the king too many times to go unnoticed or unpunished in Macbeth's eyes. After all the guests have left, Macbeth asks his wife, "How say'st thou that Macduff denies his person / At our great bidding?" (3.4.159-160). It is inappropriate for Macduff to have repeatedly denied his presence when it is either expected or requested by his king, and Macbeth can no longer assume that it is an oversight or accident when he has expressly "bid" Macduff to come to him.