I would accept this if - I had a similar experience just a few months ago in February. I took my MacBook Pro into the same store with a similar problem - connectivity - once the "geniuses" plugged it in, it took 20 minutes to boot up. At first they said it was the logic board, then it quickly progressed to the whole computer being fried. They replaced it free of charge (given that it was only six months old!) and could not tell me why this had happened.
And like I said, now everything's working just fine. What gives?
You have to understand that when a problem develops with a computer, it's not aways a quick and dirty diagnosis. One part may fail, leading in turn to other parts failing. The initial tests, like the Apple Hardware Test, may have shown a logic board problem, and with a logic board acting up, other components connected may not be able to be tested properly (at least not with the same tools) because their operation relies on the motherboard. In turn, whatever caused the motherboard to fail may have cause THOSE parts to fail also, or perhaps it was a domino effect.
I'm quite certain that if there was a problem with the staff or the store, then there'd be a plethora of others having the issue. I mean fer crying out loud… they outright replaced your first MacBook at no charge. There's no financial motivation to be screwing with you, or anyone. You may have gotten bum luck with 2 lemons. It happens. There also may well be a problem with the environment you are using your MacBook in. If you are in a building or area with unreliable power service, prone to surges or fluctuations in voltage, then THAT could be leading to damaging your computer. But we won't know for sure what it is from sitting here at home. If you don't trust the Apple geniuses, take it somewhere else.