But according to Google Translate the phrase "five seconds" could be translated as "beş saniye" therefore if Google Translate is correct in some cases the word "seconds" can be translated as "saniye", it depends on the phrase or sentence.
That's true; Turkish puts nouns in the singular after numbers and most other counting expressions: birkaç saniye "a few seconds", beş saniye "five seconds".
Also, general objects are usually in the singular, according to https://www.duolingo.com/comment/7736911 - so something like "he counts seconds" might be "saniye sayıyor".
But if "seconds" stands by itself (as in this exercise), then only "saniyeler" works, I think.
Yes, or saniyeden, or saniyeyi, or saniyem, or .....
It's a loanword from Arabic -- those don't always follow the rules of vowel harmony the way native Turkish words do.