Being a native-English speaker, I would never say in the bus. However, the preposition on also sounds odd when we compare the meaning as it means something is in touch with the ground and open also (not always). The preposition in means we are surrounded. One interesting point is that in English we always use the preposition on with public transport, for example: on the bus, on the train, on the plane and on the airplane.
One day a friend of mine (from India) he asked me:"Why we use the preposition on instead of the preposition in?" I couldn't answer the reason behind this. But I said to him I am used to it and since my childhood I have been speaking this. However, I also wanted to confirm this, so I went to my grandpa and asked him. He told me some reasons which he believed could be behind this. He said to me: "In the old days buses were open so it started from there, and all are the public transport so we have to pay the fare and we use the preposition on for the rent " He also mentioned these are the reasons he believes, but he was enough confident so I trusted him.
If you are from India, it will sound odd to you as it sounded odd to my friend also. But please keep in mind English doesn't work the way as your respected language works.
Let me add one more thing here, I could say in the bus but there must be different conditions for example: if a bus is not moving at the moment and we are using that bus as a room, so I could say we are in the bus, but if the bus is moving and I am traveling I would never say in the bus.
Let me make it more clear. If a bus driver is driving and at the same moment someone calls and asks him: "Where are you?" if he is driving then he must say on the bus, now let's say he is resting and someone calls and asks him: "Where are you?" in this case he could say I am in the bus and having some rest as the bus not traveling at the moment.
I hope, it clears the air.