Documents seen by Times Higher Education show that there were serious concerns about how options for the school were considered during an 18-month process to determine the future of the University of London institution.
The decision to become part of UCL was backed by 12 votes to eight during a council meeting held last month, despite separate surveys of staff and the academic board showing that a majority of respondents were opposed to the change.
Since the council vote, a public row has erupted over how merger options were investigated and whether staff views were adequately taken into account.
In one development, it has emerged that the academic board saw the formal "offer" by UCL just 90 minutes before a ballot on the proposal last month.
The fact that votes from the final ballot of the governing council were counted privately has also elicited anger.
Meanwhile, official records show that the institution's audit committee voiced strongly worded concerns last year about the management's exploration of the school's options - but the comments were later watered down in a revision of the minutes.
The original minutes - from a meeting in July 2010 - stated that members of the committee were "critical" of work done to assess the merger option.
They judged that "it did not provide assurance that the project was adequately managed or resourced" and that there was "no coherent plan".
Three months later, the committee removed the most explicit criticism from the minutes - a week after the governing council suggested that such "strongly held concerns" should have been raised with its chair, Liberal Democrat peer Lord Clement-Jones of Clapham.
The chair of the audit committee, Mollie Bickerstaff, resigned the following month.
Tensions over the handling of the school's Strategic Options Review - which also considered a merger with King's College London - led in June 2010 to members of the academic board passing a motion of "no confidence" in the leadership of the school's dean, Anthony Smith.
However, two days later the council passed a motion expressing "full confidence" in Professor Smith. It said it "deeply regretted" the earlier vote and rejected a separate call by the academic board for a vice-dean to be appointed.
The school is expected formally to become part of UCL by 1 January 2012. Staff have been assured that they will not face redundancy or an erosion of terms and conditions.
Lord Clement-Jones said any suggestion that the process leading to the merger decision was conducted improperly was "ill-founded".
"The process was conducted entirely properly and thoroughly from start to finish. We have reached a carefully reasoned and researched decision about our future, in which all those involved have been consulted at every stage," he said.