Shouldn't this be "Jeg spurgte dig om du havde spist mit æble."
The same goes for the English translation - shouldn't past perfect be used in the second part of the sentence?
In this context the past perfect and the past simple convey the same information. So no.
I agree, and when I wrote that in English it was accepted.
Can hvis be used in place of om for the meaning of 'if', or does it have to be 'whether' as well?
No. Unlike English, Danish tends to keep "om" and "hvis" separate. Only use "om" if you could sub in "whether" and have the sentence still make sense.
Ah I see, thank you.
That’s living with roommates for ya.
There's one in every office.