Claire Howell, who has also been Alex Salmond's personal performance adviser, was behind the Play-Doh talk aimed at motivating pro-independence campaigners.
One senior source dismissed the session as "cod-Harvard rubbish".
Yes Scotland, led by former BBC head of news and current affairs Blair Jenkins, has strenuously denied rumours of financial problems.
The speculation was fuelled by the recent departure of two senior members of its team: director of communications Susan Stewart and operations chief, Jacqui Caldwell.
The spotlight has since been thrown onto the early expenditure decisions by Yes Scotland and whether these choices have put pressure on funds. A key figure in the setting up of the campaign group was Howell, a psychology guru who helped the SNP come up with "positive" messaging.
She famously told the Nationalists to drop the word "independence" in favour of "independent", and she has also advised Plaid Cymru and former footballer Stan Collymore.
At Yes Scotland, she interviewed potential staff members and was instrumental in coming up with the independence "ambassador" programme.
However, sources close to Yes Scotland queried the decision to hire Howell, who, one insider said, "does not come cheap".
At one meeting, Howell reportedly gave all the participants items including Play-Doh and string. They were told to make something with the Play-Doh that symbolised what they were trying to achieve.
One SNP MSP said he was "not a fan" of Howell's techniques, while another said he thought some of her ideas could be seen as "gobbledegook".
A source close to the campaign said the presentation was "cod-Harvard rubbish", adding that hiring too many directors and consultants like Howell had not been a good use of the budget.
It is also believed that targets set early on, such as securing one million signatures, may have distorted the campaign group's priorities.
Howell stopped working for Yes Scotland about three months ago. She is the chief executive of the Really Effective Development Co, which offers courses in "personal and organisational development".
A spokesperson for Better Together said: "If you want to know just how messed up things have become in Alex Salmond's independence campaign, just picture Blair Jenkins and his directors sitting about a room while a highly-paid guru gets them to imagine their future using only a child's toy."
A spokesman for Yes Scotland said the Play-Doh exercise had been a 10-minute "ice-breaker" at the beginning of a meeting, adding: "We know the No campaign is hardly a barrel of laughs, but Yes is a campaign built on optimism, aspiration and opportunity.
"An occasional modicum of lightness amid the serious business of winning independence is no bad thing."
Howell did not respond to a request for comment.