Luckily we woke at 5am and were able to witness the beautiful sight, but after 9am (breakfast) it was covered by clouds and couldn’t be seen for the rest of our stay.

Can is a defective verb in English. It doesn't have all the usual forms that a normal verb would. The infinitive is "to be able", the future form is "will be able" and the past forms are "could" or "was/were able." Your customer was talking about the past, so he should have said "We were able to witness the sunrise."

He meant to say "we WERE able to witness" (past tense). There is no difference between "we can" and "we are able to". He also meant to say "and WAS missed for THE duration of OUR stay".