These systems came to put farmers in a cycle of debt largely because they were obligated to borrow from and sell to one person. That person, especially if he were unscrupulous, could ensure that the farmer would remain permanently in debt.
For example, a sharecropper might have to buy seeds and other things from a local merchant (or even from the person whose land he was using) on credit. He would do this so as to be able to plant a crop and survive until the crop was ready to be sold. The seller could set the price for these necessities. When the crop was ready to be sold, the same person would often buy the crop from the sharecropper.
An unscrupulous person could easily manipulate the system. He could charge high prices for supplies and pay low prices for crops. He could impose fees or high interest rates. By doing things like this to poor farmers who lacked education or power, the merchants/land owners could keep the sharecroppers in permanent debt.