It's important to note that the Assistant only scans messages which reach the inbox. If you have server-side rules which are moving messages to folders before they can reach the inbox, they will be missed by the Assistant.
If you find an email that the Assistant missed, you can tag (and correct) it by following these steps:
- Open the email you would like to tag
- Tap the three dots in the top right
- Tap "Add to Assistant"
- Tap the folder you would like to add it to