Both your examples that do not have hyphens are words with negative prefixes. Words that include a negative (or positive) prefix will usually be written without a hyphen.
Examples: antimatter, indecisive, unwilling, probiotic, and nonaggression.
If the word includes an adjective that is neither directly negative or positive but is instead otherwise descriptive, then you should include a hyphen.
Examples: strong-armed, evil-minded, ill-adviced, and well-intended.
"well" is a borderline case, but it is not 100% positive. It's between neutral and positive, not one of those words you would use as a prefix in the same sense that you use pro, un, in or anti.
I hope this makes sense.
EDIT: Upon reading the above answer I now realize thereThere are further prefixes that are neither positive or negative but still should not include a hyphen. I don't think it would be productive for me to quote the full list but words like extraordinary, infrastructure and transatlantic certainly seem to prove my theory a bit flawed. The point remains, however, that there are certain prefixes that are usually used without hyphen.