The newspaper has said the postponement of a dedicated helpline, emails which look fradulent but are actually real, delays in successful applications being processed and the requesting of documents which people don't have all contributed to people missing out.
HMRC has ensured everyone eligible to receive the tax break will get it.
The government's Marriage Allowance allows certain married couples to save up to £212.
This is how it works: every person gets to earn £10,600 before paying tax; this is called the Personal Allowance. If one person in a married couple earns less than this, they can transfer £1060 of their Personal Allowance to their spouse, making their tax-free allowance bigger instead.
It amounts to a saving of £212, however a partner can only transfer all or some of their Personal Allowance to their spouse if they earn £42,385 or less.
The Christian charity CARE welcomed the Marriage Allowance when it was brought in last year, saying it wanted the government to go even further and allow married couples to transfer their whole £10,600 Personal Allowance to their partners, rather than £1060 - ten percent of it.
HMRC said: "No one will miss out on the Marriage Allowance because of difficulties with online verification. People can apply at any stage in the tax year and get the full entitlement regardless of when they claim.
"For anyone who has trouble using GOV.UK Verify, alternative options are available, such as HMRC security checks. In the unlikely event they are still unable to confirm their identity online, they will be given a phone number to call to complete the application."