A stray bullet fired into a media tent at the equestrian venue and a controlled explosion near the finish line of the road cycling threatened to overshadow the opening day of action at the 2016 Olympics.

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Even as organisers scrambled to investigate both issues, they were also having to promise to redouble efforts to shift unsold tickets and improve long queueing times amid angry complaints from those who had not been able to enter venues in time to watch the action.

While there was an upbeat mood in the city and organisers were pleased with the reaction to Friday’s opening ceremony, empty seats in many venues and long queues to get into others soon caused frustration and delays.

The most dramatic incident of the day came as eyewitnesses reported a bullet from a 5.56mm assault rifle pierced the roof of the media tent and fell to the floor near a Team GB press officer and a British photographer working for the British Equestrian Foundation.

The venue is next door to a media base and there was speculation that it may have accidentally been fired from there. A Rio 2016 spokesman said: “We are aware of the incident and monitoring the investigation by the security forces. No one was hurt.”

At Copacabana, as crowds gathered to watch the denouement to the men’s cycling road race, there was a brief commotion when bomb control officers arrived suddenly to detonate a suspect package about 150 yards from the finish line. “The security services found a suspicious package … and as a precaution decided to perform a controlled explosion,” said a Rio 2016 spokesman.

Officials said there was no impact on the race, which was at that point only halfway through. The suspect package was believed to be a small bag.

On the morning after the opening ceremony the night before, largely well received by the Brazilian media and public, organisers hoped to maintain the momentum. But huge swaths of empty seats visible in the gymnastics, boxing, handball, rugby sevens and hockey arenas as the action got under way detracted from the picture postcard backdrops on show elsewhere.

On Copacabana, fans faced huge queues to enter the beach volleyball arena while others waited in line to buy tickets. Meanwhile the action started in front of largely empty stands, although they were much fuller later with Brazilian athletes in action.

While some queues were good-natured, at others fans became angry at having to endure lengthy security queues. “I don’t believe it. It’s absurd, ridiculous,” said Natalia Carvalho, 28, a Rio resident who had wanted to see Brazilian gymnast and medal hopeful Arthur Zanetti compete.

Games organisers blamed the situation on a lack of coordination between various groups of security personnel, including the police, Games staff and private security firms. The Rio 2016 director of communications blamed it on the fact “the systems did not talk to each other”.

In a later statement, organisers said: “We apologise to any spectators who have had to queue on the first day of competition. We are fully aware of the problem and frustration it causes. We requested that the relevant authorities increase the speed and effectiveness that people can enter the park by requesting more employees to work on the x-ray machines.

“Following improvements the lines returned to normal by mid-morning. We appreciate the patience and understanding shown by fans and will use this experience to improve for the forthcoming days of competition.”

The Deodoro Stadium in the north of the city was almost entirely empty at 11am when rugby returned to the Olympics, except for a few small bands of travelling fans cowering in the shade. But it filled up a little before Brazil’s match against Great Britain, as a few hundred home fans turned out to cheer their team.

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At the morning swimming heats at the Aquatics Centre on the Olympic Park in Barra, about 20km from central Rio, the stands were roughly a third full. Venues started to fill up as the day went on and in previous Games, notably in Beijing, there have been empty seats in the first few days and stands have become fuller as the fortnight has gone on.

But there remains substantial scepticism over the official figure of 80%, or 4.9m, tickets having been sold. As revealed by the Guardian earlier this week, organisers outlined plans to give away ticket to schoolchildren. The first tranche will involve around 240,000 tickets at less popular sports such as rugby sevens and golf.

“As we have already reached 100% of our revenue target, where we have places available for some sessions, we will give the opportunity to students of our education programme, Transforma, volunteers, and other partner projects, as part of our engagement effort,” said a spokesman.

“We are conducting the first Olympic Games in South America and we want to take this opportunity to bring the sports and the athletes closer to the warmth of the young Brazilians.”

Organisers have also accelerated their advertising campaign to sell tickets for less popular sports under the slogan “There is emotion in every place”.

A spokesman said that there was a daily acceleration in sales and that they were relying on the fact Brazilians traditionally bought tickets at the last minute.

However, the website shows that tickets remain available not only for the football and less popular sports but for some of the blue riband events on the track and in the pool.