Under normal circumstances, if you let the villager finish the task, and you see the tree growing in the orchard, it will continue to grow until it matures and produces fruit. If you interrupted the villager who was carrying the fruit, or if your computer's system clock was adjusted (or is not stable), you will see problems with the game.

Since you're very early in the game, it might be best to start over, unless you really like a challenging start.