Yes it creates issue. I am facing same issue with canara bank because two different customer profiles are linked with same mobile number. It's not letting me to register for the app.
But if OP doesn't want App access, then it's easily possible through branch.
Connecting with IVR will not be such a big issue, as IVR asks you to validate through DOB, Account number, customer ID, Debit card, credit card Which will different for both accounts even though they are linked to same mobile number.