Simpson had been named as the Dockers' flying emergency for their trip to Sydney to face the Swans but, in Lyon's words, "dropped his bundle" and failed to make the flight.
Earlier on Saturday, football operations manager Chris Bond told AFL.com.au Simpson had "failed to meet certain club requirements … and as a result was not available at selection at either level of football this weekend".
Lyon was initially reluctant to discuss Simpson's position and was unsure what the club had released publicly.
But the head coach eventually attempted to explain the situation, stating Simpson has previously had plenty of troubles not of his own making, but was clearly in the wrong this time around.
The 20-year-old, who is from a remote town in Western Australia, played one game last season before being used as the sub in last week's win over Essendon.
"He's had a difficult 18 months," Lyon began.
"Really I should be talking about the game, but I'll indulge you because it's topical - he has a number of family, cultural and attitudinal situations to work through.
"He'd done enough to be picked but, in this case, clearly Josh was disappointed about being out of the team so he's basically dropped his bundle.
"In previous times, Josh has gone home for cultural reasons and they might be family illnesses, western medicine versus traditional medicine, there's all of that.
"He's also a young father with two children, so there's a lot of pressures there and his background, he hasn't walked out of [prestigious Perth school] Hale with a silver spoon in his mouth.
"He comes from 500 kilometres north-west of Perth and he's been through trying circumstances in his life.
"Therefore we're trying to build a base and nurture and work with Josh and also at times discipline and encourage Josh, to be able to handle the rigours of AFL football.
"He was able to play last week, but even last week there were some cultural issues that saw Josh return to [his home town] Mullewa during the week.
"When you put all that together, it's really trying circumstances for us as a football club.
"Sometimes you're trying to do what the education system, families, mentors, elders and the government can't quite do.
"We're working through all those things with Josh."
Once Lyon returns home to Perth following Saturday's 17-point loss to the Swans, Lyon intends to sit down with Simpson and his manager Jason Dover to discuss any possible punishments.
Lyon is sticking by the midfielder for now but said his future really rests in Simpson's own hands.
"In this particular instance, it's been attitudinal and taking your bat and ball and going home," Lyon said.
"No I haven't ran out of patience, we're here to support the person and challenge the action or the behaviour.
"We'll clearly come together as a football club with leaders and Josh and his manager and talk about potential ramifications and how he needs to earn the trust back.
"I hope that helps."
Pushed further on his absence from the team flight, Lyon replied: "Let me clarify for you – he was supposed to fly and didn't turn up.
"We’re talking about a kid that's played two games.
"I certainly don't get seduced by talent.
"But all the resources in the world, no one will leave our football club without being fully supported, fully resourced and given every opportunity.
"If you end up not being with our football club, you've actually chosen that in the end.
"Let's hope we don't get to that point."
Twitter: @AFL_JD
