The congress working committee cut short the vande mataram to just only the first stanza, because other stanzas says that how Hindus of Bengal (as the song was composed for Bengal) defended their motherland from Muslim and British invaders.
When Vnde Mataram was accepted as the national song in 1950, by the Constituent Assembly, no Muslim league or Maulavi issued any Fatwa over it. Then what has happened now?