By all means, top it up. Even better, find a container which holds the
exact volume, or a combination of containers. That way you don't need to
dilute or otherwise change the wine. You can also make up a small ullage
by adding clean glass marbles, though this complicates racking. In any
event, exclude almost every mililiter of air from the container (leave
some space for temp changes & expansion).
Too late? Not at all. As long as there are no off odors, you're in fine
shape.
