There is a situation where they capture a gun nest and take a hostage. They don't have any recourse but to kill him or let him go.
Tom Hanks makes a moral decision to let the soldier go. Later - that soldier kills one or more of Tom Hank's men. [I don't recall the details, but I remember Tom Hank's expression when he kills the guy]
Because it's TH and Spielberg, I am going to lean toward this was an intentional message delivered to the subconscious of a generation through the power of the big screen. Let me explain.
The moral dilemma is a common one - maybe one of the ultimate dilemmas for anyone who has served in a martial field. What right do I have to kill my enemy when he is not a direct threat?
Then the movie, after blitzes of action, feelings of family and of nation, interludes of duty, revenge, sorrow;
now the movie brings this 'forgiven enemy' back to kill characters we have come to like.
And TH maybe has that realization 'I should have killed him' - or maybe you did in the audience too.