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I'd say there was a flaw in the system
There seem to be two errors, rather than systematic flaws - Yates failed to take responsibility for his own TUEs (and despite what @hippy says, I think it's an athletes responsibility to check his own paperwork), and having offloaded the admin to his team, the team cocked up.
He might still be in trouble if the UCI/CADF refuse to grant him what would be in effect a retrospective TUE by imposing a minimal sanction. You don't automatically get a TUE for terbutaline just because you have asthma, you also have to demonstrate that you need terbutaline rather than one of the other drugs which doesn't need a TUE.
Well fairy nuff then, if he actually has asthma then I guess it's understandable.
In that case though I'd say there was a flaw in the system.
@andyp prejudice? Yep probably. Maybe if we can go a season/month/week without a single doping scandal in cycling I'll start to feel differently but until then...