Encountering "There is more than one bundle with the CFBundleIdentifier value" while trying to upload

Question

I'm unable to publish my app.

I've been building this modular project for a while now, and it was working perfectly. Until I had to publish it.

Every time I try to upload it to the AppStore, It says upload failed with the following errors:

ERROR ITMS-90685: "CFBundleIdentifier Collision. There is more than one bundle with the CFBundleIdentifier value 'com.mouris.mario.ModuleName' under the iOS application 'AppName.app'

ERROR ITMS-90206: "Invalid Bundle. The bundle at 'AppName.app/Framworks/ModuleName.framework' contains disallowed file 'Frameworks'."

And these 2 errors are repeated for all my modules.

I've handled modules in the following way:

1. Create a new framework.
2. Add it inside the main workspace.
3. Add the module to the main project's Frameworks, Libraries, and Embedded Content. (I think this is the problem)

What am I doing wrong here? Should I be using CocoaPods to handle my dependency management? And if so how?

Thanks in advance.