I am playing at freecivweb.org with the Classic ruleset.
I had 1 turn left of Armistice with an AI. His attitude towards me was Uneasy.
Next turn I find we are automatically at Peace and:
Several of his Riflemen in my territory are disbanded <-- TOTALLY MAKES SENSE
A Transport of mine (with 2 Engineers aboard) in his territorial waters is disbanded <-- Not being the Transport a unit with Attack power, I don't know if it makes sense
Several Freighters of his in my territory are not disbanded <-- DOES IT MAKE SENSE? Especially after my Transport (similar unit?) has been disbanded
In Classic ruleset, all ships are considered military units (like, they can carry troops). Non-military ones that are not disbanded are Settlers, workers, traders, Explorers, diplomats and leaders. Your Engineers are not disbanded, they just unluckily sunk.