The BBC's Nick Hope said areas high in the stands at the sold-out event were full but several hundred dearer seats lower down were not filled.
Locog said some accredited seats - for press and media - were empty.
"We're looking into who should have been in the seats and why they weren't there," a spokeswoman told BBC News.
The Queen and the Duke of Edinburgh visited the Aquatic Centre during the morning session while 14-time Olympic gold medallist swimmer Michael Phelps scraped through to Saturday night's final of the 400m individual medley.
Sports correspondent Nick Hope said the number of empty seats was the only negative aspect of the session.
It did not harm the atmosphere, which at times - particularly around the British performances - was deafening, he said.
But it meant Olympic organisers still had some work to do, he added.
Meanwhile, tennis fans have complained to the BBC over queues to get into Wimbledon on Saturday morning, saying a ticket office was closed because the key to open it had been lost.
Locog has yet to respond to requests for a comment.
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