"And the people that were there saw that there was none other boat there save the one into which the disciples had entered, and that Jesus went not into the boat, but His disciples." [v.22]
And why is John so exact? Why didn’t he say that the multitudes having passed over on the next day departed? He desires to teach us that Jesus allowed the multitudes to suspect what had happened–if not openly, then in a secret manner. For he says, "They saw that there was none other boat there but one, and that Jesus went not into it with His disciples."
And embarking in boats from Tiberias, they "came to Capernaum seeking Jesus." [v. 24]
What else then could they suspect, except that He had arrived there by crossing the sea on foot? For it was not possible to say that He had passed over in another ship. For the Evangelist says, "There was one [boat] into which His disciples entered." Still, when they came to Him after so great a wonder, they did not ask Him how He crossed over or how He arrived there. They did not understand this great sign. But what say they?
"…Master, when did You come here?…" [v. 25]
We should not think that the "when" is here used by them in the sense of "how." But it is worth while also to notice here the uncertainty of their impulses? Those who said, "This is that Prophet" and were anxious to" take Him and make Him a king," now no longer admire Him for His former deeds, but demonstrate their astonishment when they have found Him. They sought Him, desiring again to enjoy a table like the first.
Under the guidance of Moses, the Jews passed over the Red Sea. But that case is widely different from this. He did all with prayer and as a servant, but Christ with absolute power. There when the south wind blew, the water yielded so as to make them pass over on dry land; but here, the miracle was greater. (Exodus 14:21) For the sea retaining its proper nature so bare its Lord upon its surface, thus testifying to the Scripture which says, "Who walks upon the sea as upon a pavement." [Job 9:8].
And with reason, when He was about to enter into stubborn and disobedient Capernaum, did He work the miracle of the loaves, as desiring not only by what took place within, but also by the miracles which were wrought without the city, to soften its disobedience. For was it not enough to soften even any stone, that such multitudes should come with great eagerness to that city? Yet they had no such feeling, but again desired food for the body; for which also they I are reproached by Jesus.
Let us then, beloved, knowing these things, give thanks to God for things of sense, but much more for things spiritual; for such is His will. He gives the former because of the latter, leading in by these the more imperfect sort, and giving them previous teaching, because they are yet gaping upon the world…
From St. John Chrysostom’s Commentary on the Gospel According to St. John, Homily 63, NPNF, s. 1, v. 14, pp. 357-358.