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
<VirtualHost *:80>
        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
</VirtualHost>
                                                                        For anyone who want to achieve the same in 2018 this really helped me:
https://www.phusionpassenger.com/library/deploy/apache/deploy/python/
I know it is off topic, but I found this question like 20 searches before I found the link to the Description from Passenger....
How ev's here is an excert from the tutorial:
<VirtualHost *:80>
    ServerName www.phusion.nl
    DocumentRoot /websites/phusion/public
<Directory /websites/phusion>
    Allow from all
    Options -MultiViews
    # Uncomment this if you're on Apache >= 2.4:
    #Require all granted
</Directory>
Alias /subapp /websites/secondapp/public
<Location /subapp>
    PassengerBaseURI /subapp
    PassengerAppRoot /websites/secondapp
    PassengerAppType wsgi
    PassengerStartupFile passenger_wsgi.py
</Location>
<Directory /websites/secondapp/public>
    Allow from all
    Options -MultiViews
    # Uncomment this if you're on Apache >= 2.4:
    #Require all granted
</Directory>