By save as template informaton of the page get lost, e.g. permissions. To avoid this, use powershell command:
Use this command to backup a site collection
Backup-SPSite -Identity "http(s)://your-site-collection-url" -Path "C:\backups\your-site-collection-backup.bak"
It's important to use an absolute path as -Path parameter.
Then create a new web application and then run the following command
Restore-SPSite "http(s)://your-new-web-application-url" -Path "C:\backups\your-site-collection-backup.bak"