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It certainly can - I've seen the examples. If the page loads and it's clear that the content is not the point, but rather the layout is pushing people toward the ads, then that page can get a negative Panda score.
The problem is that fixing the situation apparently doesn't lift the negative Panda score, not even the next time that Panda is "run". So clearly, this ad factor is only one of many ingredients in the mix.
I think panda is a miserable failure because it tries to mix in the pot too much things the algorithm can't evaluate properly.