iOS build got rejected by Apple

I have tried to upload the iOS build in test-flight but apple rejected the app showing multiple issues within the app. The app is developed with React Native 0.62.0, running well locally in both release and debug mode. All the issues they raised is within nodemodules which are there since the creation of the project.

Issues with: hermes-engine, node-notifier, babel-jest and metro-core

Is there someone who have faced the same issue?

Some part of response from Apple:

Dear Developer,

We identified one or more issues with a recent delivery for your app, "Gaskap" 1.0 (1000). Please correct the following issues, then upload again.

ITMS-90680: Invalid directory - The bundle Payload/gaskap_23808.app/gaskap-23808/node_modules/electron/dist/Electron.app is not contained in a correctly named directory. It should be under 'Watch'.

ITMS-90680: Invalid directory - The bundle Payload/gaskap_23808.app/gaskap-23808/node_modules/electron/dist/Electron.app/Contents/Frameworks/Electron Framework.framework is not contained in a correctly named directory. It should be under 'Frameworks'.

ITMS-90680: Invalid directory - The bundle Payload/gaskap_23808.app/gaskap-23808/node_modules/electron/dist/Electron.app/Contents/Frameworks/Mantle.framework is not contained in a correctly named directory. It should be under 'Frameworks'.

ITMS-90680: Invalid directory - The bundle Payload/gaskap_23808.app/gaskap-23808/node_modules/electron/dist/Electron.app/Contents/Frameworks/ReactiveCocoa.framework is not contained in a correctly named directory. It should be under 'Frameworks'.

ITMS-90680: Invalid directory - The bundle Payload/gaskap_23808.app/gaskap-23808/node_modules/electron/dist/Electron.app/Contents/Frameworks/Squirrel.framework is not contained in a correctly named directory. It should be under 'Frameworks'.

ITMS-90680: Invalid directory - The bundle Payload/gaskap_23808.app/gaskap-23808/node_modules/node-notifier/vendor/mac.noindex/terminal-notifier.app is not contained in a correctly named directory. It should be under 'Watch'.

ITMS-90171: Invalid Bundle Structure - - The binary file 'gaskap_23808.app/gaskap-23808/node_modules/electron/dist/Electron.app/Contents/Frameworks/Electron Framework.framework/Versions/A/Helpers/chrome_crashpad_handler' is not permitted. Your app can’t contain standalone executables or libraries, other than a valid CFBundleExecutable of supported bundles. Refer to the Bundle Programming Guide at https://developer.apple.com/go/?id=bundle-structure for information on the iOS app bundle structure.

ITMS-90171: Invalid Bundle Structure - - The binary file 'gaskap_23808.app/gaskap-23808/node_modules/hermes-engine/osx-bin/hermes' is not permitted. Your app can’t contain standalone executables or libraries, other than a valid CFBundleExecutable of supported bundles. Refer to the Bundle Programming Guide at https://developer.apple.com/go/?id=bundle-structure for information on the iOS app bundle structure.

ITMS-90171: Invalid Bundle Structure - - The binary file 'gaskap_23808.app/gaskap-23808/node_modules/babel-jest/node_modules/fsevents/build/Release/fse.node' is not permitted. Your app can’t contain standalone executables or libraries, other than a valid CFBundleExecutable of supported bundles. Refer to the Bundle Programming Guide at https://developer.apple.com/go/?id=bundle-structure for information on the iOS app bundle structure.

ITMS-90171: Invalid Bundle Structure - - The binary file 'gaskap_23808.app/gaskap-23808/node_modules/electron/dist/Electron.app/Contents/Frameworks/Mantle.framework/Versions/A/Mantle' is not permitted. Your app can’t contain standalone executables or libraries, other than a valid CFBundleExecutable of supported bundles. Refer to the Bundle Programming Guide at https://developer.apple.com/go/?id=bundle-structure for information on the iOS app bundle structure.

ITMS-90080: The executable 'Payload/gaskap_23808.app/gaskap-23808/node_modules/electron/dist/Electron.app/Contents/Frameworks/Electron Framework.framework' is not a Position Independent Executable. Please ensure that your build settings are configured to create PIE executables. For more information refer to Technical Q&A QA1788 - Building a Position Independent Executable in the iOS Developer Library.

ITMS-90080: The executable 'Payload/gaskap_23808.app/gaskap-23808/node_modules/electron/dist/Electron.app/Contents/Frameworks/Mantle.framework' is not a Position Independent Executable. Please ensure that your build settings are configured to create PIE executables. For more information refer to Technical Q&A QA1788 - Building a Position Independent Executable in the iOS Developer Library.

ITMS-90080: The executable 'Payload/gaskap_23808.app/gaskap-23808/node_modules/electron/dist/Electron.app/Contents/Frameworks/ReactiveCocoa.framework' is not a Position Independent Executable. Please ensure that your build settings are configured to create PIE executables. For more information refer to Technical Q&A QA1788 - Building a Position Independent Executable in the iOS Developer Library.

ITMS-90080: The executable 'Payload/gaskap_23808.app/gaskap-23808/node_modules/electron/dist/Electron.app/Contents/Frameworks/Squirrel.framework' is not a Position Independent Executable. Please ensure that your build settings are configured to create PIE executables. For more information refer to Technical Q&A QA1788 - Building a Position Independent Executable in the iOS Developer Library.