Yes in general

But in this case they knew it was a special case and should have informed the other parts of PayPal so this would not happen.

So this is not a good defense

I am not defending them at all, their total disregard for their customers, and lack of courtesy make them in my book one of the most awful companies to work with or patronize, but usually organizations of this gigantic scale are compartmentalized, and work in silos, and thus you have to figure it out yourself, or through an insider, how to navigate the bureaucratic maze, and accomplish the task at hand and not be disheartened with the initial frustrating response that you might get from the first line of contact with them.

It honestly doesn't really matter. That's a plausible explanation, but the customer shouldn't have to care / make special allowances because this is a big company with lots of people. It either does good things or it doesn't, and in this case it didn't.