The card is simply put back and the library or pile or cards is shuffled again.
Under C.R. 701.19a, to shuffle a library or pile of cards means to "randomize the cards within it so that no player knows their order". Thus, if any player looked at one of those cards in the process, that library or pile is not considered shuffled, and the card looked at must be shuffled back in accordance with the rules. See also M.T.R. 3.9, this thread, and this thread.
To shuffle a deck, it doesn't matter what it looks like when you started.
Put the card into the fastest space you can, (still aligning the card's face etc.) then shuffle. If this wouldn't give you a random pile, then your "shuffle" is not a shuffle.
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If a card accidentally flips over while shuffle where should I put it?
Under C.R. 701.19a, to shuffle a library or pile of cards means to "randomize the cards within it so that no player knows their order". Thus, if any player looked at one of those cards in the process, that library or pile is not considered shuffled, and the card looked at must be shuffled back in accordance with the rules. See also M.T.R. 3.9, this thread, and this thread.
Put the card into the fastest space you can, (still aligning the card's face etc.) then shuffle. If this wouldn't give you a random pile, then your "shuffle" is not a shuffle.
Awesome avatar provided by Krashbot @ [Epic Graphics].