This is a known compromise that comes with hyphenation. The hyphenation feature works by inserting soft-hyphen characters at every possible hyphenation point. They are typically invisible, and should only show up at the end of a line if the word wraps.
Unfortunately, not every editor is smart enough to properly handle soft hyphens. Text copied from your web page will include soft hyphen characters. Some programs will display a space instead of a soft hyphen. Some may display actual hyphens. And it may break spell check even if the characters are displayed correctly. If you want hyphenation on the web, you must use soft hyphens. If you use soft hyphens, other programs may not like copied text.