The Arizal held a view that Yigdal should not be recited. As the ArtScroll Siddur (Nusach Sefard) puts it,
יִגְּדַל אֲלֹהִים חַי - Exalted be the Living G-d.
This song of uncertain authorship summarizes the 'Thirteen Principles of Faith' expounded by Rambam [Maimonides] in his Commentary to Mishnah (Sanhedrin ch. 10), and stated succinctly in the Ani Maamin prayer (p. 194, see commentary there). They comprise the basic principles of Jewish faith. In the Rambam's view, to deny any of them constitutes heresy.
Although this song is printed in most Siddurim, many congregations follow the view of the Arizal that is not be recited.
Why was it the position of the Arizal that Yigdal not be recited?
The Wikipedia page I cited mentions that it was the Arizal's opinion that Yigdal not be recited, as the prayer it omitted in his siddur. However, it does not mention why.