Correct, there are 3 beans total, as confirmed by an interview with K&H.
(Do not click this link if you’re avoiding spoilers!!! I’m only including the link because it’s the reference for the quote I’m posting. http://tvline.com/2013/04/29/once-upon-a-time-season-2-spoilers-peter-pan-neal-wendy-emmy/ )
HOW MANY MAGIC BEANS ARE LEFT? | As the Charmings realized this past Sunday, Regina razed their hidden bean field — but not before snatching a total of three beans for her own purposes.
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