I know, this kind of things happen often. It's a good question. I think Furigana is used for two purpose. One is for helping readers to read some difficult Kanji, that is also hard for even Japanese speaker. Another is to add meanings or to explain situation exactly. In this example, when the speaker is saying ふたり, the author wants to explain　男女. But if the speaker says あのふたりのだんじょ, it sounds too long or unnatural, so the author used unphonetic　Furigana. That's why this conflict happened. It's a common way to express in Japanese, though, I know it makes Japanese learners confused.

When you're speaking of two people or a pair it would be ふたり in the same way if you were to say one person alone it would be ひとり and not いちひと。So it's not really unrelated at all.