A Home Office minister has apologised to a couple wrongly accused of entering a sham marriage, amid condemnation by politicians and human rights campaigners over the treatment of genuine couples.

A Guardian investigation found couples were being prevented from getting married and subjected to “insulting” and “gruelling” checks as part of a Home Office crackdown on sham marriages.

Couples and lawyers described wedding ceremonies being interrupted so the Home Office could question them about their sex lives, an official finding a nude picture on a person’s phone and showing it to others in the room, and dawn raids being carried out to check if couples were sharing a bed.

The latest case to emerge is that of Jeff and Julie Rose, both 55 and Canadian and British respectively, who have been together for more than a decade. He entered the UK on an ancestry visa in 2011 and the couple married in 2014.

When it came to renewing his visa, Mr Rose was given incorrect advice from a Home Office helpline, resulting in him being threatened with forcible removal from the UK. The Home Office took 20 months to reject the application – 14 months longer than its target.

In its rejection, the Home Office accused the couple of entering a sham marriage and said they had failed to prove their relationship was “genuine and subsisting”.

The couple lost tens of thousands of pounds in legal fees and visa applications as well as more than a year of Mr Rose’s salary as the Home Office prevented him from working.

Jeff and Julie Rose on their wedding day.

The immigration minister, Caroline Nokes, apologised to the couple in a letter to their MP, Tony Lloyd. Referring to a bail notice wrongly issued to Mr Rose, Nokes said: “It was not the Home Office’s intention to cause any distress in this regard and an apology was offered.”

She also apologised for the delay in processing the application.

After a protracted legal battle, the couple won their case in an immigration tribunal last month. Judge Andrew Davies condemned the actions of the Home Office, saying Mr Rose had been given “dubious advice” by the official advice line. He added: “The way in which the Home Office has dealt with this matter is, to put it neutrally, far from satisfactory.”

Rose had worked for more than four years as a key worker supporting vulnerable young people but lost his job due to the Home Office’s actions. The couple care for Mrs Rose’s elderly mother but, according to Davies, the Home Office suggested that if Mr Rose was no longer in the UK to help care for his mother-in-law she “could avail herself of care from the local authorities or NHS”.

Lloyd condemned the Home Office for its actions towards the couple. “The incorrect advice and subsequent mishandling of the case by the Home Office has been utterly devastating for Mr Rose and his wife, Julie. Not only enduring a bureaucratic nightmare which has affected their mental wellbeing but also losing his career and a substantial loss of earnings,” the MP said.

Rose said his experience with the Home Office had not only cost him his job but put stress on his relationship with his wife and other family members. “It felt like an elephant was stepping on my chest,” he said.

Gracie Bradley, the policy and campaigns manager at Liberty, said the case was evidence of flagrant disregard for the right to family life. She said the government “should focus on ending the hostile environment, scrapping ripoff immigration fees, and improving Home Office decision-making – not making life as difficult as possible for migrants trying to build lives with the people they love.”

Diane Abbott, the shadow home secretary, said: “The Home Office has given in to some of the most degrading and humiliating practices. These intrusive immigration checks at weddings, ruining what was set to be the happiest day of some people’s lives, are simply shameful. The Tories’ hostile environment knows no end.”

A Home Office spokesperson said: “All immigration applications are considered on their individual merits and on the basis of the evidence available, in line with the immigration rules.”