Muslims have grown modestly as a share of Assam’s population (from 24% to 31% in the three decades to 2001). No surge explains the latest violence, although the Muslim population of western Assam is growing faster. In some villages the Bodo are now a minority. They say they feel swamped by Muslim immigrants.

However, the conflict is not primarily about religion. It is about land. The Bodo hold land in common. The Bengali-speakers are settled farmers, anxious to establish private-property rights as protection against dispossession. In 2003, after a long, violent campaign for autonomy, the Bodo got their own Bodo Territorial Council, on whose turf outsiders may not own property. The Bodo consider all Muslims outsiders—hence the dispute at the mosque.
This sounds an awful lot like Mindanao, though of course in Mindanao Muslims and animists were swamped by Christian settlers. These situations can produce extremely intractable conflicts, especially if government is perceived as aiding or siding with the immigrants, and if no action is taken until the settlers are well entrenched and approaching (or have attained) majority status.

If the settlers are in fact illegal immigrants the government will have some basis to act, but I'd guess they'll need to act sooner rather than later.