I agree with you, Steven, that whether the player bet a single chip or multiple chips, I would probably handle this in the same way.
The single chip scenario though will probably occur the most frequently, in my experience, when the player believes that he is putting out an oversize chip when in fact he has mixed up the denominations and has put in one of a lower denomination then intended
("oh, I thought that was a 5000 chip, not a 500 chip"). The intention is generally to call with an oversize chip, so in these situations, a ruling of a call is clearly called for.
The other situation where this occurs often is when the chip covers a previous bet, but due to a subsequent raise that was missed by a player, the oversized chip does not cover the amount needed to call. I would use my judgment here, and if the first bet amount, the subsequent raise, and the chip are all relatively small or close in value
(e.g. a bet of 4K, raise to 8K, 5K chip thrown in), especially if "call" has been verbalized, I will be enforcing a call. In more extreme situations
(e.g. a bet of 2K, raise to 50K, 5K chip thrown in, "I thought the bet was only 2K"), I would tend to bind any chips that went into pot (i.e. the 5K) to the pot, and give the player the option to top-up the call or fold.
I think each situation needs to be considered on a case-by-case basis. However, I will almost always insist that the player be forced at least to leave the chip that has already been thrown in, in the pot -- in practice, it is easy to explain to the player that chips that are placed in the pot in turn must stay in the pot.
I acknowledge there is basis for, in theory, an exception that allows for a complete retraction of a bet in the event of a 'gross misunderstanding', but I would rarely rely on this to grant a full "refund", except perhaps in exceptional situations where the dealer and/or previous bettor(s) are at fault:
e.g. bet of 4K, an all-in raise to 50K that was whispered by a player but none of his chips were pushed forward and no all-in button is used, and the dealer admits that he heard the all-in but did not announce 'all-in' to the table, and then a player at the other side of table throws in 5K unaware of the intervening all-in raise ... in this example, I would likely allow a full retraction of the bet.
Unfortunately, whether you decide to force a call, allow the player to fold and forfeit the chip, or even allow a complete retraction of the bet, there is really no way of preventing the angle in which a player feigns weakness and then decides to "reluctantly" call the full bet. This is typically done when a player has a strong hand that he wants people to think is weak, hoping that faking his "mistake" will induce a squeeze, or future calls from the opponent. Note that once the player claims to have made the mistake, the question of whether the player really did screw up or not will immediately enter the minds of the other players, and no ruling that the TD makes can alleviate that uncertainty.
So the real interesting issue in my view, then, is if you are aware that the player has a history of playing this and other angles, is it appropriate for the TD to inform the players of the table to this fact to try to give at least some protection to the other players at the table? A somewhat analogous situation occurred at EPT Madrid (discussed here:
http://www.pokertda.com/forum/index.php?topic=453.0). Food for thought...