What does an unclear reference mean?

An unclear pronoun reference occurs when it's not clear which noun a pronoun is replacing. Example:

Jack and Jake stopped by his father's office. (Whose father's office was it, Jack's or Jake's?)

Now, if Jack and Jake are brothers, it would say:

'Jack and Jake stopped by their father's office.'

If it was Jack's father, you could say:

'Jack stopped by his father's office with Jake.' (or conversely, if it was Jake's father)