You want to do something in pursuit of your religious beliefs, and the state prohibits that thing. You go to court and assert your fundamental right to φ under the right to religious freedom. [Note: φ is the symbol for the Greek letter Phi, and in philosophy, it indicates a generic act.]
Completely separate from this, denominations and sects of religions sometimes sue the state claiming interference in 'matters of religion.' (Article 26) The question now is the meaning of 'interference.' What can it possibly mean, if states literally control the finances of temples, set guidelines as to who can be a priest, and decide which language the prayers are to take place in?
There’s also a third category of parties that show up in disputes. Sometimes, the state isn't limiting your religious freedom -- your community is doing it instead. What happens when the right to individual religious freedom contradicts the right of the religious denomination to manage their own affairs 'in matters of religion.' The parties here are not individual/group v. state, but individual/subset v. group. This is sometimes called an internal dispute. As Bhatia states the question in his paper, 'in what manner should a Constitution that guarantees the freedom of religion to both individuals and communities, mediate the claims of religious groups against the claims of their constituents?'