This has been observed with castling as well, including in posted games:
http://www.chess.com/forum/view/general/glitch2
En passant in game replay
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In this game (http://www.chess.com/livechess/game.html?id=1277553), on the move 18. ...fxg3+, the pawn on g4 that got en passant'd does not disappear on the page linked to.
It showed up fine during the game so it's no big deal, just reporting a bug.
Don't think it's a browser issue.