What are you uploading to PhoneGap Build? You should only upload the contents of your "www" folder and the associated "config.xml" file.
Does that mean the error message is displayed when the project is too big and if the project is in the wrong format?
No; it just means that your upload is too big. If you upload a CLI project including platforms/, you're pretty likely to run into the 50mb limit because a lot of stuff ends up in there, but it's stuff that PGB doesn't need. (In fact, PGB is apt to go wrong if you supply it, because there will be multiple www directories.)