The interview on Sunday prompted widespread accusations around the interrogation, with many suggesting the prime minister had not been challenged on a series of false claims he made.
Those visiting the BBC website's complaints page since the interrogation are greeted with a message at the top featuring a link to a form in which viewers can raise objections specifically around The Andrew Marr Show.
But after listing the date and channel of the show, the message also includes the statement: "Some viewers have complained Boris Johnson was interrupted too much and the interview was biased against him."
No reference is made to potential grievances about the handling of Mr Johnson's repeated falsehoods during the interview.
The message – versions of which also appear for other programmes, and seem to be used whenever a substantial number of people complain about any given issue – appear intended to make it easier for people to register their complaints.
When a large enough number of people make the same complaint about a BBC programme, the website also allows people to sign up to receive updates about the broadcaster's response without having to go through the full complaints process.
But the fact that system now means the BBC's own website is encouraging visitors to defend the prime minister and attack its own presenter has prompted criticism and suggestions the notification could result in a skewed response to the interview.
"This is next level trolling from the BBC," Labour activist Liam Young said on Twitter, in a post that had been shared hundreds of times.
"If you go to make a complaint about The Andrew Marr interview with Boris Johnson it prompts you to complain about their own presenter and to defend the Prime Minister... wtf?"
The BBC said such messages appeared on the page when there were a substantial number of similar complaints and that the system had been introduced as a way of allowing all them to be more easily handled, rather than to suggest specific complaints.
"If we are already receiving high volumes of complaints about a specific issue, using an automated registration system can be the most efficient way to handle further similar complaints and ensure complainants get an appropriate response – people are free to make other complaints in the usual ways," a BBC spokesperson said.
The Andrew Marr interview with Mr Johnson had proven controversial even before it began.
The BBC had initially said it would not allow him on the programme unless he kept to a commitment to an interview with Andrew Neil as well – but the broadcaster later relented and allowed the Marr interview in the wake of the London Bridge terror attack.
It comes amid increased scrutiny of the BBC's role in the election. The broadcaster has been forced to apologise for a number of mistakes, including editing out the sound of an audience laughing at Boris Johnson during a debate.
The BBC has responded to complaints about its interviews with Mr Johnson in the past using the same complaints website. Last week, it posted a specific response to complaints the prime minister had been too strenuously questioned when he appeared on Radio 5live near the beginning of the election period.
"The BBC believes political figures and others in positions of responsibility should be given the opportunity both to explain their thinking on matters of public concern and answer criticisms of it," it wrote in its response.
"The job of BBC presenters is to put forward the questions likely to be in the minds of our audience, and to challenge our interviewees when a point needs to be clarified."
On the same day, the BBC also posted a wide-ranging response to complaints about perceived bias in the broadcaster's coverage of the election.
"We’ve received a range of complaints about BBC News, suggesting elements of our general election coverage display bias for or against a range of political parties," it wrote in its summary of people's complaints.
In its response, it said that "BBC News does not take any position in its reporting", and that the corporation is "is independent of any political interests, and our news agenda would never be influenced by any outside organisation".