EDIT: Just to make it clear, I refer to the modern state but I mean what could have happened in the past that would make them not claim it.
Well, the current modern nation state only dates back until 1911 when they boldly declared independence, seizing their opportunity while the Manchu regime failed. However China never recognised that independence, continuing to consider Mongolia as under its jurisdiction; this included attempts by the Republic of China to establish dominance. Even Russia, who supported the move to independence, would only recognise them as 'autonomous'; in 1919 Mongolia lost autonomy under China and was effectively occupied, until the People's Revolution of 1921, with support from Soviet Russia, which both established the current nation state of Mongolia, as well as brought it into the sphere of Soviet influence.
However, the borders were to a large degree determined by China and Russia's desire for a buffer state. The current Mongolian nation state was never in a position, politically or militarily, to officially claim the province of Inner Mongolia.