Because a strong wind
ἥ τε θάλασσα ἀνέμου μεγάλου πνέοντος διεγείρετο.
John did not mention that Jesus wanted to be alone to pray as in Mark, chapter 6: 46-47, and Matthew, chapter 14:23, did. John, however, said that the sea (ἥ τε θάλασσα) became rough or agitated (διεγείρετο) because a strong wind (ἀνέμου μεγάλου) was blowing (πνέοντος). Matthew, chapter 14:24, also mentioned the troubled waters. He said that the boat of the disciples was far from the land, many “stadiums” σταδίους from the shoreland (τὸ δὲ πλοῖον ἤδη σταδίους πολλοὺς ἀπὸ τῆς γῆς). The waves tossed the boat (ἀπεῖχεν βασανιζόμενον ὑπὸ τῶν κυμάτων) and the wind was against them (ἦν γὰρ ἐναντίος ὁ ἄνεμος). In other words, they were in a little trouble. In Mark, chapter 6:48, Jesus saw that they were straining at their rowing oars (καὶ ἰδὼν αὐτοὺς βασανιζομένους ἐν τῷ ἐλαύνειν). They had an adverse wind against them (ἦν γὰρ ὁ ἄνεμος ἐναντίος αὐτοῖς). In other words, the disciples in this boat were in a little trouble. Have you ever been on a boat that was in a little trouble?