In the report's Executive Summary, the EPA stated, "Natural gas systems were the second largest anthropogenic source category of CH4 emissions in the United States in 2012 with 127.1 Tg CO2 Eq. of CH4 emitted into the atmosphere. Those emissions have decreased by 25.8 Tg CO2 Eq. (16.9 percent) since 1990." But, a paper published in Science states that a study of the emissions data indicates the actual emissions may be as much as 50% higher than what is estimated by the EPA. Based on these figures, that would be an approximately 63 Tg CO2 Eq of extra CH4 emissions and that would be greater than the total reduction of 25.8 Tg CO2 Eq since 1990. However, according to the EPA report, total methane emissions decreased from 632.2 Tg CO2 Eq in 1990 to 564.4 Tg CO2 Eq in 2012. That is an overall decrease of 67.8 Tg CO2 Eq and that is greater than the estimated increase resulting from the natural gas industry.
The study that calls the EPA figures into question was "Methane leaks from North American natural gas systems," published February 14, 2014 in Science and was written by a team headed by A. R. Brandt of Stanford University. The paper summary says,
Natural gas (NG) is a potential “bridge fuel” during transition to a decarbonized energy system: It emits less carbon dioxide during combustion than other fossil fuels and can be used in many industries. However, because of the high global warming potential of methane (CH4, the major component of NG), climate benefits from NG use depend on system leakage rates. Some recent estimates of leakage have challenged the benefits of switching from coal to NG, a large near-term greenhouse gas (GHG) reduction opportunity (1–3). Also, global atmospheric CH4 concentrations are on the rise, with the causes still poorly understood (4).
They conclude that there is more methane being released than the EPA estimates, but the amount is still better than the equivalent emissions that would be emitted by coal-fired power plants.
It's never easy.