The reason is because the song worships the country, the mother. According to the Muslim religious leaders then, those stanza's were not ok, they should respect the country, but worshipping was another story, they worship only Allah so they were removed 3 of the offending stanza's in 1930's.
Fast Forward to 1990's. New set of Muslim leaders claiming to be true'er muslims banned even the remaining 2 stanza's that currently constitute Vande Maataram. BJP when it came into rule, made it an issue, some places made it mandatory.
Dont remember the name of the organization, they came out and created a fatwa against "Vande Maataram" Fatwa here means banning its constituents from singing it.Now it is upon the followers of the religion to decide if they feel the 2 stanza's actually are against the teachings of Islam and whether to obey the religion over singing the national song.
70 years ago, the parent of BJP had the same position as what the BJP/RSS today has, but the Muslim relgious folks certainly have become more hardlined than their predecessors in 1930's, Frighteningly most of them went on to form a flourishing nation called Pakistan