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Most riders, when they take a bottle from the crowd, pour it over their head/neck to cool down with it, as they know drinking it runs the risk of contamination.
And the implication is that if they (are witnessed) drinking from a bottle from the crowd then it's because they knew they could trust the bottle because it was actually an unofficial team handup, hence the penalty.
How true that is I've no idea.
Is it controversial though? If no commissaires saw him drinking from the bottle, and there is no tv evidence, it would be harsh to penalise him. Most riders, when they take a bottle from the crowd, pour it over their head/neck to cool down with it, as they know drinking it runs the risk of contamination. That is probably what Bardet did.