Can't merge or retrain?

[Korlon]

Did the settlement in question have the unit you're trying to retrain as an option for recruitment? For example, if you're trying to retrain your triarii, you'll most likely have to go to Roma for that. Trying to retrain it in Capua would only grant you the upgraded equipment as you can't recruit triarii there.

About the siege weapons, no idea. I've noticed this too. Just something wrong with the game I suppose.