That is not the case. Princely states were given the right to decide which country they wished to join. Junagarh decided for Pakistan and was occupied by India using force.
Hyderabad remained independent till September 1948. They even had a representation in the UN. On 13th September 1948 Indian army invaded Hyderabad and occupied it.
Just like how Maharaja Hari Singh of Kashmir decided for India and Pakistan tried to capture it by force.