Fitness trainer Sarah-Jane Walls incurred an automatic penalty of £750 after filing the annual accounts of her Glasgow-based company six months late.
They were due to be lodged with Companies House by April 1, but Ms Walls only signed off the accounts on October 1.
If the paperwork had been another day late, the fine would have been £1500.
A Companies House spokesman said: "The penalty has now been issued and is on its way to the registered office [of Transdynamic Ltd]."
Yes Scotland last night blamed an oversight.
When she was appointed to the advisory board of the cross-party independence campaign in July 2012, Ms Walls was described as a businesswoman and "certified professional personal trainer and weight management specialist" with a passion for pilates.
A member of the pro-Yes Business for Scotland group, she was given a greater role in Yes Scotland last month when she became the leader of its work on "stakeholder engagement".
Ms Walls founded Transdynamic Ltd in July 2011 and is the sole director and shareholder.
In an online profile, Ms Walls says the company is cutting edge, and an "exciting new company bringing training and technology together".
However, its two-year-old website carries only a logo and the words "coming soon".
The company has the £30,000-a-year lease on a four-storey townhouse on Park Circus Place in Glasgow, where Ms Walls runs a spa, fitness and pilates centre called The Residence Glasgow.
Transdynamic Ltd is currently appealing against the £44,000 rateable value on the property.
Besides Transdynamic Ltd, the building is home to two other companies of which Ms Walls is the sole director and shareholder, The Residence Glasgow Ltd and Reformer (Scotland) Ltd.
The address is also used by Musecom Solutions Ltd, which is run by her father-in-law and brother-in-law.
All the firms except Transdynamic Ltd filed their annual accounts on time.
Despite its lease and business rate appeals, a Yes Scotland spokesman claimed Transdynamic was "dormant" and did not trade "as such".
He said: "The delay in filing accounts was an oversight. Any penalty will be paid."
He denied that Ms Walls was an embarrassment to the Yes campaign.
Under the 2006 Companies Act, a private firm such as Transdynamic Ltd incurs a late filing penalty of £750 for being three to six months late filing its accounts, and £1500 for being over six months late.
Yes Scotland's spin doctors, Hay McKerron Associates Ltd, fell foul of the same law as Ms Walls last month when they failed to file their first set of annual accounts on time.
The two men behind the firm, Gordon Hay and Ian McKerron, did not sign off their accounts until three days after the September 9 deadline.
They blamed their accountant for the slip, and said he would pay the automatic £150 fine.
Another Yes Scotland board member, SNP Euro candidate Tasmina Ahmed-Sheikh, was last year served with a notice by sheriff officers acting on behalf of planners at Glasgow City Council.
She and her husband were ordered to apply for retrospective planning permission after an unapproved extension was added to their home in Newlands, on the southside of the city.
The council paperwork said the work was "a significant breach in planning control".