The argument concerns only “this region.” Whether apples were cultivated in other regions does not affect the reasoning of the argument.

The author overlooks the fact that, 5,000 years ago, cultivated and wild apples might have been more similar in size compared to their relative sizes today. We cannot rely on their relative sizes today to conclude that the smaller apples of 5,000 years ago were not cultivated.

The argument concerns remains of apples in a particular region that are the same size wild apples. The existence of other apples sized in between wild/cultivated doesn’t weaken the argument. So the author doesn’t need to assume there are only two sizes for apples.

There is no premise that contradicts the conclusion. The conclusion is that apples probably weren’t cultivated 5,000 years ago in this region. None of the premises makes the conclusion impossible to be true.

(E) describes circular reasoning. None of the premises assume the truth of the conclusion. The premises include comparison between sizes of apples today, and a claim about sizes of remains of certain apples. The conclusion is about whether those apples were cultivated.