A series of mishaps and near-misses included stray bullets, robberies, an attack on a media bus, serious crashes in the cycling road races, empty seats, booing crowds, broken toilets in the Athletes' Village and a pool mysteriously changing color.
In competition, Usain Bolt, Michael Phelps and Simone Biles lit up South America's first Olympics with standout performances. Rugby sevens, new to the Games, captured global audiences. The host nation only won seven gold medals while Britain claimed more gold medals than China or Russia.
"Compared to other Olympic Games, it looked a bit like the smallest show on earth," said professor Simon Shibli, head of Sheffield Hallam University's Sports Industry Research Center in England.
"A symbol of all of that has been the diving pool turning green, and no one really knowing what was going on or what to do about it," Shibli said.
"Most people interact with this event by watching it on television," said Stefan Szymanski, professor of sport management at the University of Michigan in Ann Arbor.
"As a TV experience thus far, it's fine. But the one thing that is really noticeable is how many empty seats there are," said Szymanski. "To TV viewers, this is something puzzling and not always good for generating interest."
John Coates, vice president of the International Olympic Committee, told the BBC the Rio Olympics had been "the most difficult games we have ever encountered."
"I wish there were bigger crowds," Coates said.
Although Rio organizers stressed about 84% of tickets had been sold, some sports such as women's soccer were staged to a handful of spectators early on in the competition while even some track and field sessions were poorly attended.
Well-attended events, such as the men's pole vault and the women's beach volleyball finals, were overshadowed by partisan crowds booing the competition.
France's Renaud Lavillenie, the defending pole vault champion, was reduced to tears after he was twice subjected to a chorus of boos during his battle for the gold with Brazilian hope and eventual winner, Thiago Braz da Silva.
It led to sharp condemnation from IOC president Thomas Bach, who called the crowd's behavior "shocking" and "unacceptable at the Olympics."
Rio 2016 spokesman Mario Andrada said organizers would "intensify" its dialogue with local fans "to make sure that we behave as fans in a proper and elegant manner, without losing or passion for sport."
It was to deaf ears as there was more booing when Germany played Brazil in the women's beach volleyball finals. The Germans kept a cool head and took the gold.
Following London as the host city of what then IOC president Jacques Rogge called the "happy and glorious Games" was always going to be a tall order.
The £9.3 billion ($12 billion) London Olympics were held with venues delivered on time and under budget to mostly sold-out stadia with enthusiastic crowds at all events.
Still, the start of the Rio Games was similar to what London 2012 organizers experienced, with empty seats and security concerns taking center stage.
Whereas London quickly managed to right the ship by bringing in the military and making more tickets available after some events in the first weekend had empty seats, Rio organizers never came up with Plan B.
"They had the World Cup in 2014, they were barely ready for that and that was just one sport," Shibli said.
Hosting 28 different sports in one city "was something of a recipe for a certain amount of disorganization and inability to pull it off in the same style that more developed economies like the U.K. or China would be able to do," Shibli said.
'Our time has come'
It had all looked so different in Copenhagen in 2009, when Rio beat Chicago, Madrid and Tokyo in the 2016 bid race.
"Our time has come," a beaming Brazilian president Luiz Inacio Lula da Silva said.
Some 50,000 locals on Copacabana beach wildly celebrated Brazil's arrival on the global stage as an ambitious emerging economic superpower.
"If you give us this opportunity, you will not regret it," Lula said.
But what Lula had promised would be a Games full of "passion, happiness and creativity" turned out to be anything but.
Seven years later, Brazil is mired in a massive corruption scandal that led to the suspension of president Dilma Rousseff while it grapples with the worst economic crisis since the 1930s.
While much of the pre-Games focus had been aimed at the trash-ridden and polluted water sports venues, the outbreak of the Zika virus and fears venues and infrastructure wouldn't be ready on time, a spectacular opening ceremony suggested skeptics were wrong.
"We haven't got evidence of lots of people falling down with the Zika virus or getting infected by polluted water in the sailing competition," Szymanski said.
"I anticipate people looking back on this and saying: 'for all the negatives, they pulled it off, they did it.' And that has pretty much been the narrative of every Olympic Games that has even been," he added.
"Fantastic competition. Fantastic venues. Enormous global audiences. And a fantastic legacy for the people of Rio and Brazil," IOC spokesman Mark Adams wrote in an email, when asked to sum up Rio.
Brazilian taxpayers may disagree. The Rio Games cost $4.6 billion, or 50% more than planned.
"Academic research tends to show that the impact of the Olympics in economic terms is negligible," Szymanski said. "The Rio and Brazilian economy will neither be much better off nor much worse off than it would have been if they had never held the Games."
The experience in Rio may lead to the IOC going for "safe options" in Asia, Europe or the US, both Shibli and Szymanski said.
The 2020 Games will be held in Tokyo while the 2024 bid race has been narrowed down to Paris, Rome, Budapest and Los Angeles.
"What they want is something which will be a lot closer to their brand values and a lot safer for their sponsors," Shibli said. "This has not been an unqualified success."