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"I wonder why."
than a
"Why?"
and I think it's less of a question and more of a statement.
Looking at Google it appears to be about half and half split between ? and 。
Also the ? is a relative newcomer to Japanese. In explicit questions, as long as you have the か at the end you don't need the ? at all.
Anyway, long answer short, it might be best to unlink this sentence from "Why?" and link it it to a new translation with "I wonder why."