Darcy’s discoveries are ‘mortifying’ (humbling, humiliating) because they are wounding to his pride. The appearance of ‘pride’ in the title of the novel alerts us to the significance of this aspect of his character. Darcy is a man who is especially proud of his social position, family connection, and self-sufficiency. At the Meryton assembly in chapter 3,
he was discovered to be proud; to be above his company, and above being pleased
Let’s look at the passage from the question in detail.
he made it clear to himself and his friends that she hardly had a good feature in her face
It seems that Darcy and his friends—that is, Mr. Bingley, Caroline Bingley and Louisa Hurst—had been disparaging the attractiveness of the young women they had met at the assembly, and that Darcy’s contribution to the game was to criticize the appearance of Elizabeth Bennet. But no sooner had he done so,
he began to find it was rendered uncommonly intelligent by the beautiful expression of her dark eyes
This is his first ‘discovery’ and he finds it ‘mortifying’ because it makes him a liar and hypocrite, and because according to his self-conception, Elizabeth’s social position ought to place her beneath him. Later on he will describe “his sense of her inferiority—of its being a degradation—of the family obstacles which had always opposed to inclination”.
Though he had detected with a critical eye more than one failure of perfect symmetry in her form, he was forced to acknowledge her figure to be light and pleasing, and in spite of his asserting that her manners were not those of the fashionable world, he was caught by their easy playfulness.
Here the important words are ‘forced’ and ‘caught’. Darcy believes that his self-control and self-sufficiency ought to make him invulnerable to Elzabeth’s charms, and that he should be able to impose his principles on his heart, but he finds that it is otherwise. The narrative later says that Darcy “had never been so bewitched by any woman as he was by her”, and in his botched proposal of marriage, he will tell Elizabeth that he “liked her against his will, against his reason, and even against his character.”