I am trying to run to run django and flask on the same apache server.
WSGISocketPrefix /var/www/wsgi
        ServerAdmin name@email.         
         
I'm not sure if this would solve the problem, but have you tried changing the order of your script alias so that /app1 is found before / ?
WSGISocketPrefix /var/www/wsgi
        ServerAdmin name@email.com
        ServerName  domain.com
        ServerAlias www.domain.com
        DocumentRoot /var/www/
        LogLevel warn
        WSGIDaemonProcess apache processes=2 maximum-requests=500 threads=1
        WSGIProcessGroup apache
        Alias /media /var/www/media/
        WSGIScriptAlias /app1 /var/www/flaskapps/app.wsgi
        WSGIScriptAlias / /var/www/djangoapps/django.wsgi