According to many Church Fathers, Christ was not, in fact, referring to the faith of the Apostles, but rather to the faith of the man who came to them when He gave this teaching.
Theophylact's commentary on the previous verses (Matthew 17:16-18):
Do you see how the man has shifted the blame for his own lack of faith upon the disciples, saying that they were too weak to heal? The Lord, therefore, is shaming him for accusing the disciples, saying "O faithless generation," that is, "It is not so much the fault of the weakness of the disciples as it is of your lack of faith, which, being great, has prevailed over the equal measure of their strength." He rebukes not only this man, but everyone who lacks faith, even the bystanders.*
Thus, Christ's teaching was for all who heard Him, and not just the Apostles (to whom the teaching seems not to have even been directed).
Cyril of Alexandria (378-444) provides the same interpretation of the parallel passage in Luke (9:37-43), though the reference to the mustard seed appears later in a different context:
The father therefore of the demoniac was rude and uncourteous: for he did not simply ask the healing of the child, and in so doing crown the healer with praises, but, on the contrary, spake contemptuously of the disciples, and found fault with the grace given them. For I brought him, he says, to Thy disciples, and they could not cast it out. And yet it was owing to your own want of faith that the grace did not avail. Don’t you perceive that you yourself are the cause that the child was not delivered from his severe illness?
* The Explanation of the Gospel According to St. Matthew (tr. from Greek; Chrysostom Press, 2008), p.149