On Rosh Chodesh, the tefillin are taken off before davening Musaf. There are two reasons for this practice: 1) The Kedusha of Musaf in many shuls begins with keser yitnu (offering of the crown, so to speak, to Hashem). It is improper for another crown--the tefillin--to be on the head at that time. 2) Tefillin are not worn on Yom Tov. Since Yom Tov is an ois, it is not necessary to have another ois of tefillin. Although Rosh Chodesh is not a Yom Tov, mentioning the korbonos is akin to an ois and therefore the tefillin are removed.
[סעיף יג וס"ק סא; ביאורים ומוספים דרשו, 77]