No word appears in more than one list at any single main entry. Some words have slight variations in meaning. If they are used one way, they are synonymous with an entry word; if they are used another way, they are merely closely related. To avoid confusion, such words have been entered in a main entry's synonym list only.
For example, nice is in the synonym list at pleasant where the shared meaning is "giving pleasure or contentment to the mind or senses." Nice is also in the synonym list at amiable, where the shared meaning is "having an easygoing and pleasing manner especially in social situations." If you go back to pleasant, you will find amiable among the related words. So it would stand to reason that nice, having the same meaning as amiable, would also be entered in the related word list at pleasant. Since it's already in the synonym list, however, it was left out of the related words.
Some words can have two meanings that are opposite of each other—or nearly so. Nervy can mean both "fearless" and "fearful, timid." Thus, at the thesaurus entry for bold, where the shared meaning is "inclined or willing to take risks," nervy might qualify as both a synonym and an antonym (or near antonym). And, indeed, nervy appears as a synonym, along with adventuresome, adventurous, audacious, daring, dashing, emboldened, enterprising, gutsy, hardy, nerved, venturesome, and venturous. Although the near antonym list contains fearful and timid as expected, nervy is left off the list. Again, this is to avoid confusion.