If you start AI, open a project file that is read-only, make a change to the project, and then close AI, you get prompted to save changes. So far, so good. If you click Save, AI pops up a message box saying "Error opening file <filename>" and then closes, discarding your changes.
I think in this case AI should stay open, giving you a chance to either remove the read-only flag from the file or save the project somewhere else. This is what most other applications do.