As quarterbacks have become efficient at calling audibles, defenses have had to adjust their strategy.
The main thing a quarterback looks at when determining an audible is the alignment of the defensive backs and linebackers. Are they in Cover 2, Cover 3, or Zone? Are the corners playing man-to-man? Based on what that quarterback sees, he will make the decision to stay with the play that was called, or change the play at the line of scrimmage. What's a defense to do?
Disguising coverage (also called stemming) allows a defense to give the impression they are running a different defense than they actually are. For example, the safeties will line up in what looks like cover 3, and as close to the snap as they can, they will move into position, or "stem," to play cover 2. Or the corners might line up like they're covering man-to-man and as the ball is snapped, they'll move into position for zone coverage.
This change has made it more difficult for quarterbacks to call the perfect audible. But defenders have to be careful not to get caught out of position when the ball is snapped.