"Why is she coming to nose into my master's private business?" ... "Why isn't she leaving us be?"
-Winky, remembering the unfortunate event
Bertha Jorkins comes to her boss’ house with papers for him to sign and overhears Winky speaking to the hidden Barty Crouch Jr. in the kitchen. She hears enough to figure out that Crouch Sr. is hiding his supposedly dead convict son in his home, and confronts the elder Crouch when he arrives home. Crouch Sr. responds by removing the memory of Winky and Crouch Jr.’s conversation from Jorkins’ mind with a memory charm so powerful it permanently damages her memory.
According to Sirius, Bertha Jorkins was never terribly sharp (GF27). So, it seems likely that she would have had to overhear a great deal of conversation to catch on.
Barty Crouch Sr. rescued Barty Crouch Jr. out of love for his wife, not out of any tender feelings towards his son, so it's safe to assume that he put the memory charm on Jorkins in order to protect his own reputation rather than to protect his son.