The phone number for both pupils and parents is their username, in this case two entries of the same phone number will lock out the account they're associated with until the phone number is resolved.
How to set up parent logins for two pupils on the same system
Start by logging into the Web Admin.
Go to Learners >> Select Pupil name:
You will see the parent profile you originally setup on the first pupil, go to the second pupil profile, click "+" Contact and enter the same number, before saving uncheck send contact login details by text message - change the last digit of that phone number and make a note.
Lastly send the parent an SMS via Whatsapp or your default SMS option on your phone with the login details: