They were troubled - They were afraid. The sight was remarkable. It was sufficient to awe them. In the dark night, amid the tumultuous billows appeared the form of a man. They thought it was a spirit an apparition. It was a common belief among the ancients that the spirits of people after death frequently appeared to the living.

It is a spirit - That the spirits of the dead might and did appear, was a doctrine held by the greatest and holiest of men that ever existed; and a doctrine which the caviliers, free-thinkers and bound-thinkers, of different ages, have never been able to disprove.

And when the disciples saw him walking on the sea, they were troubled, saying, It is a (d) spirit; and they cried out for fear.
(d) A spirit, as it is taken here, is that which a man imagines to himself vainly in his mind, persuading himself that he sees something when he sees nothing.

And when the disciples saw him walking on the sea,.... It being now morning, and perhaps might have moon light; and besides, there is always more light upon the water than land; they were able to discern something like a man, walking upon the surface of the sea, but had not light enough to distinguish what, or who it was; and, moreover, had no thought of Christ, or expectation of seeing him; and the appearance of a man walking upon the waters being so unusual, and astonishing,
they were troubled, saying it is a spirit: a nocturnal apparition, a demon in human form. The Jews, especially the sect of the Pharisees, had a notion, from whom the disciples might have their's, of spirits, apparitions, and demons, being to be seen in the night; hence that rule (u),
"it is forbidden a man to salute his friend in the night, for we are careful, lest , "it should be a demon".''
They say a great many things of one "Lilith", that has its name from "the night", a she demon, that used to appear in the night, with an human face, and carry off young children, and kill them. Some such frightful notions had possessed the minds of the disciples:
and they cried out for fear, as persons in the utmost consternation, in the greatest danger, and in want of help: the fear of spirits arises from the uncommonness of their appearance; from their superiority to men in power and strength; from the enmity there is between men and evil spirits; and from a general notion of their doing hurt and mischief: hence, demons are, by the Jews, called "hurtful", or "hurting", all their study being to do hurt to men; and the same word is here used in Munster's Hebrew Gospel: add to all this, that the fear of the disciples might be increased, through a vulgar notion among seafaring men, that such sights are ominous, and portend evil to sailors; and they might the more easily be induced to give credit to this, and fear, since they were already in such imminent danger.
(u) T. Bab. Megilla, fol. 3. 1. Sanhedrim, fol. 44. 1.

A spirit. An apparition, an unreal appearance of a real person. The word is not that unusually rendered "spirit." He would appear to them at first like a dark, moving speck upon the waters, then as a human figure; but in the dark, tempestuous sky, and not dreaming that it could be their Lord, they take it for a spirit (Luke 24:37).
Cried out. In fright.