Step 1: Identify the pronoun.
The word “it’s” (it is) is a pronoun referring back to a noun mentioned earlier.
Step 2: Find the most logical antecedent.
Sentence:
\[
\text{“I put my coffee cup on the shelf next to the phone and now it's gone!”}
\]
The thing that can logically be \emph{gone} is the coffee cup.
Step 3: Eliminate incorrect options.
Phone — phones do not normally disappear in this context.
Shelf — shelves are fixed objects.
Both (A) and (B) — only one logical antecedent fits.
Hence, ‘it’ refers to
\[
\boxed{\text{Coffee cup}}
\]