Hi,
You need to strip the formatting out before copying it into Endnotes. Endnotes does not have this feature. What you probably need is a clipboard manager like Clipmate or the one from Donation Coder. These allow you to copy in plain text. You could also convert the html code by pasting it to your notepad program, or even Word can handle this if you know how to do it. The other thing you might do is use Google Scholar for your searches and in the setup to Google Scholar you can have import to Endnote links added to your search results. Import your entries from here by clicking on the import to endnote link, rather than copy and paste them. You can also import using Library of Congress by using Endnotes connection feature, but this will just work for books mostly. Copying and pasting should be a last resort and if you do it you will have to follow one of my suggestions above.Good luck.