These two sentences have different emphases.

There is a telephone in that room.

The second sentence means that the telephone emphasizes the location of the telephone in that room (in that room but not in other rooms)

Which sentence pattern to use depends on the context.

There is no difference between the two sentences if the context is not considered.

Let me give you an example. Suppose you left your mobile phone in the library. You ask the librarian if you have seen your mobile phone.

If he says there is a telephone in the room, he means that he knows there is a telephone in that room, but he is not sure if it is yours.

If it says that the mobile phone is in that room, it means that the mobile phone is in that room (he is sure it is your mobile phone)