Seriously, it's like . . . some people register with Jesse, and some just don't if they don't make any sort of impression on him. Santana is someone he vaguely recalls, but he finds her tiresome with her constant "spy!!!" jabs. She hasn't vocally impressed him on any level (see: why he remembers Mercedes and Kurt), and she hasn't interacted with him in any way that really stands out beyond minor annoyances. He just . . . doesn't care right now.
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Seriously, it's like . . . some people register with Jesse, and some just don't if they don't make any sort of impression on him. Santana is someone he vaguely recalls, but he finds her tiresome with her constant "spy!!!" jabs. She hasn't vocally impressed him on any level (see: why he remembers Mercedes and Kurt), and she hasn't interacted with him in any way that really stands out beyond minor annoyances. He just . . . doesn't care right now.