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Not under normal circumstances. I had some issues recovering damaged harddisks that had lots of errors and retries and sometimes either the USB adapter or the mainboard SATA would crap out or handle it better. But for normal copying of HDDs, both should copy the exact same data.
I second this, when a drive shits the bed a sata controller handles it better, some times with a USB adapter you mess the whole bus up and need a reboot of the machine (from using them on windows experience)
What you're describing is data TRANSFER. Bad sector detection and management is done by the drive controller firmware.