New Defender's Study Bible Notes
5:4 troubled the water. This verse is omitted in certain of the manuscripts, along with the last part of John 5:3. Because of what seems to be the unlikelihood of this cyclic miracle, most modern versions have omitted it. The problem is, however, that John 5:7 (which is in all the manuscripts), makes no sense without it. Furthermore, the great majority of the manuscripts do include all these verses. Whether the miracle seems reasonable or not to our scientific minds, the probability is that it was recorded by John in his original text, and was later deleted in some manuscripts because of the skepticism of the copyists. There is nothing impossible about the miracle, no matter how unusual it seems. Perhaps God, in view of the long absence of a prophetical voice in Israel, elected to maintain this continuing witness to His grace and power in Jerusalem, as a sort of perpetual Messianic promise, to be repeated regularly until Christ would come.
5:9 made whole. This is the third of the great creation miracles described by John. A man hopelessly crippled for thirty-eight years (John 5:5) who suddenly had perfectly sound limbs again can be explained only in terms of the creative power of God Himself. It should have been a mighty testimony to the Jewish leaders of His deity, but instead they complained because He did it on the Sabbath.