I was receiving that warning message as well when I tried to upload a new build of my app to iTunes Connect, I fixed it by adding a 1024 x 1024 icon to my res file in the phonegap.zip folder, it is named icon-512-2x.png, I also added this line to my configuration file,
<icon src="res/ios/icon-512-2x.png" width="1024" height="1024" />
Then I built it using the Phonegap Build service. When I uploaded it to iTunes Connect, I did not receive the warning message.
I followed this stack overflow question https://stackoverflow.com/questions/48236079/phonegap-missing-app-store-icon-1024x1024px-app-store-icon.
This icon needs to be uploaded via itunes connect, which seperate from the phonegap build process. If it is not then Apple will reject the binary upload.
If it does get rejected then sometimes it is quicker to create a new build, upload it to iTunes connect and then submit for approval. You will need to make sure your version is changed in the config.xml otherwise when you upload the ipa it'll get rejected as it conflicts with another version.
This process is unfortunetly very common problem with iTunes connect process. Sometimes it can be approved within the hour, other times it will get rejected and you can appeal to get it accepted. If it takes a long time to get approved then it is quicker remove it and add a new build.