You blockaded Brutii/Scipii ports? I must be misunderstanding something, because you would not be allied with them and still blockading the port, the computer would not let you blockade them. Or did you blockade all trade coming into their ports, is that what you mean?
Yes, since you attacked first, you took the town. I have done that myself before, though my personal code of honour keeps me from doing it more. I also used to send spies into allied towns to force a revolt, but I have the same issue with honour.
AI will sometimes land armies, mainly if you take Sicily as say Greece, Scipii keep bringing mainland armies to Sicily to take Messana back. Other than that, they don't do invasions much, Kydonia stays rebel for a long time usually, and Rhodes rarely comes under attack as well. Palma and Caralis do get attacked quickly.
You actually can see how a town is doing financially, send a spy into a town and it will tell you its financial status, you double-click on the town and it will be near the bottom.
As Ludens said, you are getting the armour/weapons experience upgrades only, since town apparently does not have sufficient barracks, or possibly numbers to retrain (though that usually only happens at the town level).
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