More carriers are participating in the exchanges this enrollment season as worries has subsided since the tumultuous first rollout of the exchanges last fall. HHS said earlier this fall that nearly 80 new carriers will participate in PPACA's marketplace this year, increasing the number of participating carriers by 25 percent. In total, 77 new carriers will offer coverage when open enrollment for PPACA begins Nov. 15.

"Although most insurers expect a loss from participating on the exchanges in 2014, insurers were hoping to establish a solid market share during the first three years of operation of the health exchanges," wrote Steve Zaharuk, Moody's senior vice president. "Because the penalties for not being insured increase each year under the Affordable Care Act, insurers expected that there would be significant membership growth in these plans each year and that these enrollees would be composed of healthier individuals, stabilizing the risk profile of the pool and eventually creating a profitable business for insurers. The new lower membership projection challenges this strategy."

Moody's said they think a number of factors influenced the lower projection, including a shorter enrollment period (three months versus six months last year), an increasing number of individuals who qualify for an exemption from PPACA's penalties, and increasing premium costs.

Also on Thursday, the GAO announced that enrollment for Obamacare's state-operated Small Business Health Options Program is also falling far short of government expectations. Only about 76,000 people working for about 12,000 employers had enrolled in insurance plans sold by 18 state-run SHOP exchanges, while the projected enrollment number by the government was 2 million by the end of January.

Open enrollment begins Nov. 15 and runs through Feb. 15.

Additionally, Moody's said the Supreme Court's decision last Friday to hear an appeal in King v. Burwell, further complicates participation in PPACA plans.

"A ruling against the subsidies would increase the cost of these polices to the individual, and in that case we expect a majority of the policies to lapse. Since it is likely that only those who need insurance the most would retain their polices, insurers would be faced with insuring a much less healthy population than they expected."