Threema displays only contacts who use Threema. If you know that someone is using Threema, but they are missing or are marked with a red dot, it is because of one of the following reasons:
If a contact has linked a phone number or email address to their ID that is included in your address book, the contact shows up in Threema’s contact list (provided that synchronization is enabled) and is labeled with two orange dots.
To start the synchronization process, simply tap on your contact list, drag it down and release it again. To work properly, activate the synchronization feature in “Threema > Settings > Privacy.” If you are an iOS user, make sure to grant Threema access to your contacts (“iPhone Settings > Privacy > Contacts > enable Threema”).