I seem to have too many unspent outputs for my given balance. What am I missing?
As per the comments on OP’s question

Since you made a copy of the wallet.dat file (which is an HD format), both addresses will be under the control of (both copies of) your wallet. Hence, both UTXOs will be listed when calling the listunspent command, as each wallet is able to spend both UTXOs. 

If you used a new wallet to generate a new address, and send some funds to it, then the listunspent command should function as you originally expected, as your bitcoin core wallet would not control the address you spent coins too (it would only control the change address).