Words like "special" and "exceptional" used to be (pretty-unambiguously) positive but now can also be negative because of the tendency to use them to refer to people (usually kids) who are below average in some way. "Special needs" usually refers to some sort of handicap, which is perceived as a limitation, hence negative. I'm not judging this, just explaining it.
Because people who work with special-needs kids try to never use a word that could sound negative, but people in the rest of society will still sometimes perceive these kids' situations negatively, you will get sarcastic uses of the previously-positive words, introducing ambiguity. ("Wait, is this 'exceptional' kid gifted or learning-disabled?")
You can usually tell by context. It's pretty common (in my experience) to hear somebody describe some negative situation with "oh how special", but the tone of voice tells you what is meant. The positive meanings are also still in use, so you have to look for context.