Podfile gets overwriten and some dependencies disappear

When you install some plugins that use CocoaPods, some of the libraries disappear from the Podfile.

Steps to reproduce:

1. cordova create testPods
2. cd testPods
3. cordova platform add ios
4. cordova plugin add https://github.com/aerogear/aerogear-cordova-push/
5. Open platforms/ios/Podfile and check that pod 'AeroGear-Push', '1.2.0' is there
6. cordova plugin add https://github.com/jcesarmobile/cordova-plugin-tesseract-ocr
7. Open platforms/ios/Podfile and check that pod 'TesseractOCRiOS', '~> 4.0.0' is there, but pod 'AeroGear-Push', '1.2.0' is gone

Expected:
have both
pod 'AeroGear-Push', '1.2.0'
pod 'TesseractOCRiOS', '~> 4.0.0'

It's curious that if you install them in the opossite order, this doesn't happen

In both cases, the pods.json file has the information of both pods

This doesn't happen with all plugins, so looks like an edge case. I found this two plugins where the problem is present, but it was also reported on Slack.