I’m thinking the reason Cora suspected there was magic in SB was due to Emma and Snow’s appearance in FTL – what was left of it. Adding to that suspicion is when Cora tried to get Emma’s heart, she was unable to get it and instead was repelled, surprising Cora. In addition there was her education in Rumple’s curse before he turned to Regina, which she knew about, probably more than Rumple.
Cora seems a bit savvy and is able to connect the dots easily, even when they are not apparent to anyone else.
I find it interesting that Rumple is “afraid” of Cora, even though he denies it.
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