CKEditor 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 is featured with Advanced Content Filter (ACF) which transforms and removes disallowed elements. If you paste content into CKEditor 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 will strip bold tags from the source code.