"Pragma measured the effect by comparing the volume in certain stocks with the time it takes to execute an order. Longer execution times typically result in poorer results, since a stock's price can swerve away from where it was when the order entered the market. Such an effect is known in the industry as a "shortfall.""
If you are a "long term" investor you don't sell stocks to capture a few pennies here and there. You buy at price $X and hold it for a while, maybe you put in a stop order [1] so that if the shares start heading for the floor you will automatically exit. You set a value you want to see for your 'gain' and you set a limit order [2] when the stock starts getting close. The limit fires and you exit the stock. Even if it keeps rising and rising.
The basis for the claim in the article is that some HFT house might buy your stock when it hits the limit order price, because it is predicting it will go higher and then instantly resells it for a bit more than your price. You've cashed out already (closed your position) and they skimmed a bit of cream off the top. You didn't 'lose' any money at all.
For those not familiar with stock trading:
[1] A 'stop' order tells the firm holding your stock that if the stock drops below a certain price (the stop price) to automatically sell the security. So if you buy a stock at $10/share and you don't want lose more than 20% on it you might set a stop order for $8/share.
[2] A limit order goes the other way, you tell the broker that if the stock ever gets to a certain price to sell your shares. So if you are looking for a 10% return on your $10/share stock you might put a limit order in for $11/share. (or $11.25 if you want the 'net proceeds' to be $11/share).