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Yep. Example would be having your account tied to your PayPal. It will remove regardless if you have the overdraft protection or not.

i had something like this happen with Netflix. my account at TCF Bank was low and the transaction was denied. then, apparently, Netflix tried the transaction again and succeeded, which overdrafted my account. i asked the bank what the difference between the transactions was and they just shrugged. it's possible your friend's explanation is accurate

Call the bank and ask, and consider whether she may be lying to you to protect her preferences.