No, just one army.
It's just happened again, but this time I won the second re-match, but lost key units I can't replace
I think it is because the invading army is going straight to assault the city. It loses in the field but then continues to assault the city and thus triggering a second set of battles.
I really think that once an army is beaten it must retreat rather than continue onwards. I see this behaviour with rampaging armies, that are region hopping, you beat them, but what's left continues and it takes several turns to continually chase them to beat them into non-existence.
I also think that an army shouldn't be allowed to attack a city if there is an army in the field in the region. I think this allows armies that struggle in certain terrain to avoid having to beat the field army and yet they can assault the city and avoid the terrain malus.
This behaviour is really making the game unplayable for minor powers. This along with the MP script issue is ruining a great game... MP is generally not viable because of modders and now SP is wasting my time. I'm investing a lot of time and effort in these games only to be frustrated by bad design.