The general advice is to long rest as often as possible. Any time a character says "I'm tired" or similar while exploring, this is actually indicating that they have something to talk about.
I assume, in order to get Rafael the first time you long rested, you didn't long rest until after talking to Nettie? Pretty sure the game expects you to have long rested 2-4 times before that.
This thread (SPOILERS)
https://forums.larian.com/ubbthreads.php?ubb=showflat&Number=762145#Post762145 is relevant, discussing which companions to bring to which events/conversations.