When you look at your transaction on a block explorer, you may see multiple outputs. This is because multiple coin transfers can occur in one block (and typically do), or under one transaction ID. Within the BTC protocol, there is are addresses called the "change" addresses that serves a vital function in returning unspent funds to a wallet.
Learn more about UTXOs and Change addresses here.
See this video for a detailed explanation.
NOTE: Multiple output transactions are not supported by ShapeShift at this time. These often occur if more than one user tries to exchange using the same transaction ID, like when sending from a mining pool or third-party. Reach out to our support team if you believe this has occurred with your exchange.