According to Thoreau, how can the government sometimes hinder the people?

Thoreau wastes no time getting to his feelings about government in Civil Disobedience:

I heartily accept the motto, ‘That government is best which governs least.'"

Thoreau writes that the scope of the government can be misused much in the way of the standing army:

The government itself, which is only the mode which the people have chosen to execute their will, is equally liable to be abused and perverted before the people can act through it.

Thoreau believes it is too easy for a few corrupt individuals to decide the course of the nation without the input of the people.

It has not the vitality and force of a single living man; for a single man can bend it to his will.

It’s not that he believes there should be no government but that there must be "a better government.” He believes that conscience should prevail over law.

Must the citizen ever for a moment, or in the least degree, resign his conscience to the legislator? Why has every man a conscience, then?

He goes on to say that men march off to war feeling it is wrong:

Now, what are they? Men at all? or small movable forts and magazines, at the service of some unscrupulous man in power?

Thoreau believes that our government set-up doesn’t leave much room for the individual to have autonomy, which allows for decision-making based on right and wrong.

All voting is a sort of gaming, like checkers or backgammon, with a slight moral tinge to it, a playing with right and wrong. . . The character of the voters is not staked.

He mentions slavery as an example of the ways a government can get something wrong and the majority must not prevail:

I do not hesitate to say, that those who call themselves Abolitionists should at once effectually withdraw their support, both in person and property, from the government of Massachusetts, and not wait till they constitute a majority of one. . . . I think that it is enough if they have God on their side, without waiting for that other one. Moreover, any man more right than his neighbors constitutes a majority of one already.

As with many of Thoreau’s writings, he emphasizes the importance of independent thought to a functioning society.

According to Thoreau, the government can hinder the people when it governs too much. He says, "That government is best which governs not at all." He uses the Mexican-American War as an example of this. The war, to him, is unjust, and he believes that the majority of individual citizens would not have consented to the war. Yet the government still moved forward and engaged the country in it.  
Further, he points out that the government itself never actually "furthered any enterprise": it does not keep the U.S. free, settle the western territories, or educate citizens.  Everything that has been done for the good of the country has been done by the American people—by individuals who sought to improve things—and not by the government. If anything, he thinks, the government has actually gotten in the way, in part because it can be influenced by a "single man" who seeks to "bend it to his will."