Post History

The oldest occurrence of "join issue" I can find is [from 1624](https://www.british-history.ac.uk/lords-jrnl/vol3/pp247-248), i.e., not medieval.  In fact most records of legal proceedings by that time were still in Latin - so I am far from saying that the phrase couldn't be older by a few centuries like your source suggests.

Courts like to address conflicts only after both parties have issued their positions on the conflict.  If one party takes action (requests a ruling) against another, the court is likely to order the other party to "join issue", i.e., to issue a position on each claim brought forward by the first party, while setting a deadline for that to happen.  The verb "join" does not imply that both sides would agree with each other on every fact of the case, because then they would have no conflict for the court to try; it rather implies that they the extent of their agreement and disagreement was made clear: they will be contradicting each other on the *same* issues.