The internal conflict in Liam O'Flaherty short story about the Irish civil war "The Sniper" is patriotism versus morale.
Here we have a soldier, who is a sniper, in a typical monitor duty while he is having a snack to eat. Noticing that there might be enemy fire coming his way, he gets in position to attack. After failed attempts from both sides, one enemy bullet finally gets the sniper. Conversely, the sniper is able to shoot at the enemy and kill one of the soldiers.
However, in a moment of vulnerability, the sniper curses the war and the fact that he has to be a part of it. He would have not killed a man had he needed to. He does feel remorse, and he develops a quaint curiosity to know who the man is. After all, prior to the way, he and this other soldier may have been friends, or at least acquaintances.
The sniper looked at his enemy falling and he shuddered. The lust of battle died in him. He became bitten by remorse. The sweat stood out in beads on his forehead. Weakened by his wound and the long summer day of fasting and watching on the roof, he revolted from the sight of the shattered mass of his dead enemy. His teeth chattered, he began to gibber to himself, cursing the war, cursing himself, cursing everybody.
When the sniper goes to check who it is, he is shocked to see that he has shot and killed none other than his own brother. This is a strong message about the horrors of war, and the little choice some individuals have to be or not be a part of it.
That is precisely what the internal conflict of the sniper is: He is part of something that he does not plan. He is part of an army as a result of his patriotism. He kills as a result of being a part of the army. However, he is not a warrior, nor a killer. He would otherwise turn his back to it and refuse flat out to do what he has been told.