There are so many H. Hybrids with the word 'lightning' in their name and only a few using 'lightening'. The rules for naming H. hybrids say that deliberate misspellings which could cause confusion are not allowed, so this must not have been seen as a misspelling. Perhaps it was a case of the person(s) making the official decision while reading the application being too polite and not questioning the spelling.
(By the way, I couldn't spell 'misspellings' properly without Spell Check
).