How to memorize differences between ingenious, ingenuous, and indigenous
ingenious - Latin ingeniōsus - full of intellect, superior in mind, able, intellectual, clever, ingenious
ingenuous - Latin ingenuus - inborn
indigenous - Latin indigen - homeborne
ingenuus can refer to different words in English, and that I think is the confusing part. The only way to remember is to be familiar with their usage. For me, this is not confusing because I've encountered these words so many times in books, articles, etc.
Ingenious means "clever". You can remember this because when pronounced it is pronounced "(in)genius" and genius is someone who is smart.