During negotiations throughout the week, representatives of the National Union of Journalists (NUJ) handed over a 64-page dossier which contained a catalogue of complaints from employees.
An NUJ spokesman said management were "taken aback by the evidence" and that they say they will revamp HR procedures.
Despite the positive talks, union chiefs said there was "no doubt" that workers would be prepared to take industrial action if concerns are not addressed. If strikes went ahead, there could be serious disruption to coverage of the Commonwealth Games and the referendum campaign.
Anger came to a head at the beginning of last week when it emerged that Good Morning Scotland host Gary Robertson was being axed.
The high-profile presenter, who has worked at the BBC for 15 years, was told that his contract would not be renewed in August, in a move understood to be down to cost-cutting measures.
Colleagues have questioned why bosses recently hired expensive presenters from London, including Sarah Smith, who was poached from Channel 4 to front Scotland 2014, and former Today programme co-host, Jim Naughtie.
Critics say the unrest is the latest manifestation of a "prolonged series of dysfunctional management" decisions.
The Sunday Herald understands there has even been a discussion of a vote of no confidence in the news and current affairs management.
Discontentment has been building since a raft of redundancies took place last year.
A £5 million cash injection announced last May by BBC director general Tony Hall and BBC Scotland director Ken MacQuarrie has only served to create more uncertainty, as workers are questioning how the money has been managed.
The NUJ spokesman said staff were hanging in limbo as they wait to see if bosses will address the issues. "They [management] were really shocked and surprised at the extent and range of complaints, and how widespread they are," the spokesman added.
"They have given us assurances that they will put protocol in place for dealing with work pressure, etc.
"Industrial action and possible legal action has been put on hold to see if their commitments come through.
"But people will take action no doubt if things don't change."
The NUJ says letting go of Gary Robertson was viewed as "unacceptable".
Robertson is believed to be on a "talent contract", which gives high-profile presenters freelance status and the freedom to work for different outlets. "The view is that there has been no consultation," said the union spokesman.
Crunch talks between Robertson and management are likely to take place when the presenter returns from holiday leave in the next two weeks.
The NUJ spokesman said: "When he [Gary Robertson] comes back from holiday, management will sit down with him and a representative from the union to decide his status.
"The NUJ has said to management that he should be offered a staff job. We have discussed industrial action and legal action and we are prepared to take both."
A BBC Scotland spokeswoman said: "We had very productive talks with the NUJ earlier this week on a number of issues during which we reiterated to them our commitment to work constructively with them.
"We have arranged to hold a follow-up meeting with them soon and in the meantime will continue our normal local talks as we work together to try to resolve any areas of disagreement."
When asked about Robertson she said she could not discuss "contract negotiations with freelancers".
In a survey by the NUJ, more than 50% of staff said there was friction/anger in the workplace.
One staff member said: "I don't know if the way the newsroom is run is explicitly designed to destroy the motivation, morale and mental health of staff or if that is an unintended consequence."
Staff are unhappy at the way in which outside talent has been brought in during Scotland's year in the spotlight.
The replacement of Newsnight Scotland with Scotland 2014 has also caused confusion.
Ratings bombed for the new magazine-style programme.
It has attracted fewer viewers than STV rival Scotland Tonight, with figures as low as 22,000.
Former BBC broadcaster and pro-independence blogger, Derek Bateman, said it was too late for bosses to make changes and people were now thinking ahead to the vote on September 18.
He said: "It's the latest manifestation of what's been a prolonged series of dysfunctional management [decisions].
"They can't improve, they're just dismal. I think what is really apparent to me and many other people that after September there needs to be a massive change.
"If there's a Yes I think there will be a mass clearout at executive level. They'll need to change our broadcaster into a different beast. If there's a No I think the BBC will bear a lot of the brunt from pro-independence people who feel badly let down by the national broadcaster in what should have been its finest hour."