Adding insult to injury, dark pools often use retail investors' money to increase their liquidity. Charles Schwab, for instance, sends some retail-order flow into a dark pool owned by UBS.

The Tabb Group's Johnson explains: "So the institutions are able to take a large order and park it in the pool, then let the non-educated retail flow pass through," nibbling away at it but without being able to see the large block aching to be filled or being able to affect the price being paid for the shares.

These are just niggling concerns compared with the problems such pools might bring if they continue to scarf up market share at their current rapid pace. Something ugly could be around the bend.

"As these dark pools grow, then the public—you and I—will get less liquidity in the sense of price," says Boston University Law professor Tamar Frankel, a securities and regulation expert.

"There will come a point," she adds, "where the price on the open exchanges will not be sufficiently informative, and that will hurt everybody, even the parties that trade on these dark exchanges, because the price may no longer be representative of the true value of the shares."