Translation:In my city, there are three bridges.
Yes, "There are three bridges in my town" is accepted.
I suppose the course admins chose "city" as the default English translation because of American English. When visiting friends in the States, we drove through some tiny little towns (some barely more than villages from my perspective) which had "Welcome to XX City" signs.
I think you could say that the nuance changes like this:
My town has three bridges. (the focus is on "my town")
There are three bridges in my town. (just a neutral statement about the existence of three bridges in a place that happens to be your town)
There are three bridges in my town. (focus is on "in my town")