What's unfortunately upset crew — the alien reptile? (10)
I believe the answer is:
salamander
'reptile?' is the definition.
(salamanders are mythical lizards)
'what's unfortunately upset crew the alien' is the wordplay.
'what's unfortunately' becomes 'alas' ('alas' is used to express regret).
'upset' says the letters should be written backwards.
'crew' becomes 'man' (both can mean to staff or operate something).
'the alien' becomes 'der' ('the' in German - 'alien' can mean 'foreign').
'alas' reversed gives 'sala'.
'sala'+'man'+'der'='SALAMANDER'
(Other definitions for salamander that I've seen before include "portable stove" , "Fiery spirit" , "Mythical fire lizard" , "Tailed amphibian" , "Long-tailed amphibian" .)