Since market prices are constantly changing, your trade rate is likely to fluctuate. For example, by the time blocks confirm and your trade executes, the price in ETH may have gone up in price. This happens in the stock market as well as the crypto market. ShapeShift allows you to set the maximum amount of slippage for any trade you initiate. Simply select the highest percentage you will allow to account for market slippage.
Here is a screenshot from beta.shapeshift.com which shows the different percentages you can select to account for slippage:
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The miner fee will be paid even if your trade does fail because the price of the cryptoassets had moved outside your set percentage. In general, it makes sense to put a higher slippage percentage to ensure your trade doesn't end up failing.