CKEditor 4 is a standards-compliant (W3C) HTML editor which means it corrects code if it doesn’t follow current web standards. What’s more, some browsers may have their own interpretation of HTML.
Also, CKEditor 4 is featured with Advanced Content Filter (ACF) which transforms and removes disallowed elements. If you paste content into CKEditor 4 and notice that some elements are removed, then chances are high that it was removed by ACF. For instance, if your toolbar doesn’t include the Bold button, CKEditor 4 will strip bold tags from the source code.