This issue could be because of multiple factors, normally due to access issue over the folder(like root Inetpub). User may not have sufficient permissions to create folder or application.
I would suggest you to export MSI without the web application, for this in "Select Resources" section uncheck web application and binding files while exporting the MSI.
Ideally you should not export MSI with other artifacts like binding file and web applications because these things might have different configurations in different environments. So they should be migrated separately.
To export Web Application
1) In IIS Manager(inetmgr), select your application -> Right click -> Browse
2) This will open the folder location of your application, go one level up to see the complete directory.
3) Copy this folder and take it other environments and copy it to the inetpub folder
4) Open IIS Manager and create new application using the copied folder.
5) Configure the settings(like authentication, App pool etc) as in previous environment.