The passage from Ignatius where he claims he was the disciple of John?
The passage to which you are referring is not considered to be an authentic letter of St. Ignatius and is not included in the above manuscript.
From the Catholic Encylopedia:
At intervals during the last several centuries a warm controversy has been carried on by patrologists concerning the authenticity of the Ignatian letters. Each particular recension has had its apologists and its opponents. Each has been favored to the exclusion of all the others, and all, in turn, have been collectively rejected, especially by the coreligionists of Calvin. The reformer himself, in language as violent as it is uncritical (Institutes, 1-3), repudiates in globo the letters which so completely discredit his own peculiar views on ecclesiastical government.
The convincing evidence which the letters bear to the Divine origin of Catholic doctrine is not conducive to predisposing non-Catholic critics in their favor, in fact, it has added not a little to the heat of the controversy. In general, Catholic and Anglican scholars are ranged on the side of the letters written to the Ephesians, Magnesians, Trallians, Romans, Philadelphians, Smyrniots, and to Polycarp; whilst Presbyterians, as a rule, and perhaps a priori, repudiate everything claiming Ignatian authorship.
The two letters to the Apostle St. John and the one to the Blessed Virgin, which exist only in Latin, are unanimously admitted to be spurious. The great body of critics who acknowledge the authenticity of the Ignatian letters restrict their approval to those mentioned by Eusebius and St. Jerome. The six others are not defended by any of the early Fathers. The majority of those who acknowledge the Ignatian authorship of the seven letters do so conditionally, rejecting what they consider the obvious interpolations in these letters. In 1623, whilst the controversy was at its height, Vedelius gave expression to this latter opinion by publishing at Geneva an edition of the Ignatian letters in which the seven genuine letters are set apart from the five spurious. In the genuine letters he indicated what was regarded as interpolations.
Etc, etc................