The conclusion wasn't that this was caused by HFT but because NASDAQ and the NYSE only showed trades that had a size of 100 or greater in their public feeds. Since a 100 shares of APPL is worth $50,000+, there's a lot of trades being made for less than 100 shares and, until the reporting changes made a few weeks ago, they didn't show up on the public feed. This means that trade volume wasn't being reported accurately, and that the public feed wasn't representative of the active price of a stock like APPL - which is a fairly big deal when, according to the article, 45% of APPL trades are in lot sizes of under 100 shares.
For professional traders (and here's the only place where HFT is relevant) it's not a big deal since they don't use the public feeds but instead pay for feeds from the exchanges which include all trades.
For professional traders (and here's the only place where HFT is relevant) it's not a big deal since they don't use the public feeds but instead pay for feeds from the exchanges which include all trades.