First of all, you calculated the supply that includes the reward given to the gensis block. By design, the genesis block's reward is not included in the UTXO. That is 50BTC gone alone.

IIRC, there were a few blocks that had a fork and the coins from those blocks were lost. Due to bugs in the miner's implementation, there were instances whereby the miner didn't claim the entire block reward and/or fees and that is definitely not in the satoshi range.

You have to consider that some coins were also burned by the use of OP_Return and they were removed from the UTXO of the client.