I think it's because the color green is associated with Esperanto, and a crocodile is only green on the outside. It's considered rude to speak another language in an environment where the intent is to converse in Esperanto. Some people find it jarring, and it can make it difficult to focus on the language.
Alia teorio venas al esperanta instuisto kiu havis lignan krokodilon, kaj se vi volas paroli en via denaska lingvo, vi devas teni ĝi. (https://en.wiktionary.org/wiki/krokodili#Etymology)
One day I'm going to remember the difference between the word for "need" and the one for "want". Not today though.