A German woman has been separated from her two-year-old daughter in Edinburgh after a Home Office mistake left her stranded in Dusseldorf earlier this week.

Liza Tobay, who has lived in the UK for 15 years, had taken her oldest child, a six-year-old boy, to visit his grandfather and some other relatives over Easter when confronted with what she said appeared to be “a serious administrative error”.

She is one of millions of EU citizens who, before Brexit, could just use their passport at the border, but must now prove they have “settled status” to enter the country as a lawful resident.

The first she knew of the error in the UK system was during her return on Wednesday when she tried to make a connecting flight from Munich to Edinburgh during a layover in Dusseldorf.

When she presented her passport, the border official told her they had been trying to reach her as her settled status had been “red flagged” and she and her son would not be allowed on the connecting flight.

She said she could prove she had settled status via an email but was told she could only do this through a phone app, which she did not have.

Tobay said: “I started to panic and my son started to cry. It is the first time he’s been away for five days without his dad, so he’s been homesick already and could sense something wasn’t right.”

She said she had been “up all night” researching what she could do but was unable to log into the Home Office website to see what the “red flag” was showing with her immigration status.

After resetting and logging in again, she could see the passport number recorded for her was completely wrong.

The next day, she phoned the Home Office EU settlement scheme resolution centre, and was told a “ghost number” had appeared on her account.

“He could see the photo of my passport but could see the system had generated a completely random passport number, different from the one in the picture,” she said. “They told me they are escalating it and it is to be given priority but that it might take three weeks.”

Tobay said it meant she could be away from her two-year-old for up to a month.

She said: “This situation is extremely distressing for our family. It is just awful. I haven’t slept, I haven’t eaten, I am just in shock, in autopilot trying to stay calm and do what I can to get home.

“I told them: ‘No, this is not OK, you are separating me from my child.’ I have never been away from her before now.”

She has booked a flight for Sunday but fears the Home Office will have not rectified its mistake by then.

The grassroots campaign group the3million, which has long objected to the digital immigration status, said her case was not isolated, and the length of time the Home Office took to resolve issues was “unacceptable”.

Tobay’s case has highlighted the risks of the UK’s decision to use a digital-only verification system to show immigration status, to which many objected.

The3million has said EU citizens living lawfully in the UK since Brexit should have a card or a QR code in an app to show authorities rather than having to log into a computer system.

Monique Hawkins, the head of policy and advocacy at the3million, said: “The Home Office insists a digital status cannot be lost, stolen or tampered with. We have long objected to this empty catchphrase as we keep being contacted by people suffering serious impacts from non-functioning eVisas.

“The level of error is unacceptable, but what’s worse is how long people sometimes have to wait before their problem is fixed. To add insult to injury, the Home Office denies all liability for the losses people face from eVisa errors.”

The Home Office said it had reviewed the case and been in touch with Tobay.

“The issues raised have now been resolved and there are no wider issues around the system,” it said.