I was having this issue as well, I found the answer here:

https://stackoverflow.com/a/27039447/23618150

(I develop in VSCode, the terminal inside of it is where all my commands will be ran from.)

1. Go to the IOS directory and open the xcworkspace in Xcode

   cd IOS

   open runner.xcworkspace

2. Once inside Xcode, make sure you have runner selected

3. Make sure you have the Project Runner selected
4. Under the Info, find Configurations.
5. Set all configurations to none, this includes Debug, Release, Profile.
6. Close Xcode and return to vscode.
7. I just ran pod install and it reinstalled the pods and it did not give me the warnings again. Though when I go back into Xcode and look at the configs, it automatically put them back, but I believe it is supposed to.