Archer went home instead of arriving straight in Manchester after the first Test despite COVID-19 threat.
But Vaughan did concede it was a "bit selfish" of Archer to go back home in the break between the two Tests when he needed to arrive straight at the Old Trafford ground in Manchester.
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Archer's breach could've led to the cancellation of the entire Test match and put a threat on the series. With that in mind, Vaughan said the team Archer should be the most apologetic to is not his, it is the visiting West Indies one, which has taken such a huge risk of arriving in the UK in these difficult times to help English cricket.
"It did surprise me that one player kind of went a little bit haywire, breaking the bio-bubble. The whole series is at risk if he brings the virus in the bio-bubble. It's a real problem area," Vaughan told Cricbuzz.
"Jofra has had one of those moments. It's a little bit selfish. He has probably felt a bit low. England lost the Test match and he just wanted to go home and see probably one of his loved ones. We are not quite sure why he went home. But I am guessing that's the reason."
"Should he be thrown under the bus for it? Absolutely not," he stressed. "He is a young player who has made a mistake, it's a mistake in these unprecedented times. I don't think you can really question what the players are going through mentally, having to live at cricket venues, looking at cricket grounds for 3-4 weeks. They have not got much else to do."
"I am not going to be too critical of him. It's a huge sacrifice that the West Indies team made. They came over here on June 8 and entered a Covid hot zone in the UK to get the series on. It's the West Indies that I look at, Jofra should really look at them and apologise," Vaughan added.
Archer has been slammed a lot over social media for putting his and the rest of his team's health at risk. In wake of that, Vaughan feels it's important that the cricketer's mental well-being is looked after by the team management, as he approaches a five-day isolation period and needs to twice test COVID-19 negative before rejoining the squad.
"But also, a lot of his teammates have got kids and families back home and I am sure, you look at someone like Jimmy Anderson, he lives 2 minutes from Old Trafford. He has got 2 daughters. I am sure he would have loved to nip home but these are the kind of sacrifices you have to make in a team culture," said Vaughan.
"He has broken those. As I said, I hope he is not thrown under the bus. I fear for him, he is going to be on his own in the hotel for 5 days. No one can go and visit him. It's so important that we look after Jofra Archer the person over the next few days because it's not going to be easy."
"He is probably reading everything on social media. I hope he doesn't but I am sure he will be. He will be back playing for England, whether it will be in the 3rd Test? I doubt it. But I am pretty sure he will be back for the Pakistan series in August," he added.