"The alligator is a little smaller than a crocodile."
Translation:Ο αλιγάτορας είναι λίγο μικρότερος από ό,τι ένας κροκόδειλος.
Ότι is a conjunction introducing secondary clauses, e.g. Θα πω ότι δεν το ήξερα = I will say that I did not know about it.
Ό,τι is a pronoun (primarily) meaning 'anything'/'whatever', therefore it replaces something that is implied or has already been mentioned. E.g. Θα πω ό,τι θέλω = Ι will say what(ever) I want.
Admittedly, the grammar of the sentence in this exercise is a bit complicated. Ό,τι refers to the size of the crocodile, the implied object of the verb (είναι) here: Ο αλιγάτορας είναι λίγο μικρότερος από ό,τι (είναι) ένας κροκόδειλος. With the introduction of (είναι) we have
Ο αλιγάτορας είναι λίγο μικρότερος (subject - verb - object) από
ό,τι (είναι) κροκόδειλος. (object - verb - subject)
In short, ό,τι, being a pronoun, structurally matches λίγο μικρότερος in the second part of the sentence.
Alternatively, the sentence could be
Ο αλιγάτορας είναι λίγο μικρότερος από έναν κροκόδειλο. - which is the same as in English. However, notice that with 'ό,τι (είναι)' missing, κροκόδειλος is no longer the subject of the (implied) verb and needs to be in the accusative, just like you would say 'bigger than him' (not 'he').
The word ό,τι is a very special/singular word in Greek. It has a "comma" in the middle and without it the meaning changes so it must be written correctly or it will be rejected.
In other situations, Duolingo does not reject words etc for wrong accents, comma etc.
Please see the comment by D_.. on this page. The use of ό,τι and ότι (which I'm sorry to say look so similar ) but have different meanings.
But I'm glad to say you do not need to learn all those details. Just use the Drop Down hints which show you which words to use. That's the whole secret to translating on Duolingo.
My answer Ο αλιγάτορας είναι λίγο μικρότερος από ένας κροκόδειλος was marked wrong. I don't understand why,because it was exactly the answer given by Duolingo in a previous lesson and I had noted it down to remember the nominative masculine ένας κροκόδειλος. ό,τι was not expressed. Could you please verify?