Mails from send E-mail smart service are going into recipients junk folder

I've found this can sometimes happen when there's a mismatch between the "from: email address" and the actual sender domain (which will be your appian instance), for instance when you're overriding the "sender" details with something belonging to an individual user.  Unfortunately this behavior is largely controlled by the recipient's email system and hard to control from the Appian side.