Word Relationships

Both would be "A," I believe.

1.) Eerie and Wary are synonyms, while bountiful and trusting could be seen as synonyms aswell. But all for together? Antonyms. Same goes for 2. Interesting.

No, they certainly are not! Eerie means "spooky" and wary means "cautious", so there is no relationship between them at all - they are neither synonyms nor antonyms. Nor is there any relationship between bountiful, which means "generous", and trusting.

In the first group the only two connected words that are connected in meaning are wary and trusting: they are antonyms (i.e. opposite in meaning).

In the second group the connected words are murky (which means "cloudy": you can say that water is murky when it is discoloured with mud, or that the sky is murky if it is filled with clouds and rain) and its antonym, clear.

You could argue that mottled and clear are antonyms, because a person's skin is said to be mottled if it is spotted with freckles, pimples or a rash, and clear if it is not. But this is just one specific use and I suspect that murky/clear is the pair your teachers are looking for.