You need to use a tool name MTool. Basicly this is a RPG Maker Game, and MTool is basicly a application make able the cheat but also for Debug.
So open the game using the MTool Directory, when the character answer to the phone, DO NOTHING when the Dialogue Box appeared and go in MTool and click on "View Active Event"
The tool will show you witch line of the script the game is currently are, just under the ["SceneMenager.push(Scene_MenuMessage);"] there a Controle Switches line. It will look like that: 2243: : 0;
This line is basicly the probleme, it's probably a automatic Comment Event who is trigger by the problematic switches, but it seem to not have any code readebly by the game, so you need to desactivated the switche.
Go to the "Switche" tab off the tool and go at the probematic line as mentionned earlier I have probleme with the Switche 2243 and just check/uncheck the box on the same line. In my case I was need to uncheck it.
After retour to the game and that's it, close the Dialogue box and you can play again.
Make sure to save otherwise you will need to start again.
And you musn't retour to the Phone Message Menu otherwise the game will freeze again.
If you want to download the tool, just go on this page
You must be registered to see the links
EDIT
Also sometime it doesn't work, I don't know why, but you could "Clean Event" on the Main Tab, that work every time. But usally in RPG Maker Clear an Event is temporary so be ready to use it regulary with that method. But, it also disable all Event who is occuring at the same time