We assumed that the crackers generally don't play the games they crack very much, they just play until the point where the protection they know about kicks in. Then they release a crack, believing it to be complete.
To play on this, we designed the game to break in ways that weren't immediately obvious. Most of the protection is "off-camera," affecting levels other than the one currently being played. In YOTD the object of the game is to collect eggs and gems, which are then used to open later parts of the game. The protection removed eggs and gems, so that the player could not make progress. We tried to make the game unplayable for any length of time, while at the same time making it difficult to determine exactly where things had gone wrong. If errors accumulated slowly until the game broke, the cracker would not notice such behavior so easily.
Some of these actions break the game and others are just an annoyance to the player, but if the game is difficult or frustrating to play because of the failed crack, this can be more effective than breaking completely.
By making the game behave in as many odd ways as possible, we hoped to cause a lot of confusion. The pirates wouldn't know if the crack didn't work, whether they had just failed to apply the crack correctly, or if the disk had failed to burn correctly. The people who didn't play a lot of the game wouldn't notice that anything was wrong and claim that the crack worked.