Possibly because the country you want to attack is a free city, which benefit from the Emperor's protection. Also joining the HRE was kinda bad, because the Italian states leave around 1465-70ish in the Shadow Kingdom imperial incident. Now that you've also joined, you'll get a choice to leave or stay, staying will give you negative diplomatic reputation and +3 unrest IRC, while leaving will damage your relations with the Emperor (meaning Austira unless he loses emperorship) and may cost you your alliance with him.
Thanks for the quick response. None of the provinces in the northern Italian area are free cities. Now that the 'Shadow Kingdom' event has happened none of them are in the HRE anymore so it doesn't matter. I just don't understand why a lot of other HRE members were attacking each other without Austrian interference but I couldn't.