I'm not completely sure if it was adequately explained on the show that Barnabas had an affair with Angelique BEFORE he started courting Josette. It could've been during the courtship, or he and Josette could've broken up and Barnabas could've taken refuge in Angelique's waiting arms. The reason that many people think that it began before the fact, to my knowledge anyway, is because of Lara Parker's book, "Angelique Descent", in which she explains that Barnabas came to Martinique on a business trip with his father and had a dalliance with Angelique, then dumped her like a sack of potatoes and went with her mistress, Josette.
Personally, I always thought that Angelique read more into the relationship than what was really there, but it wasn't completely her fault. Barnabas could've led her on, and could've used her for a good time when he needed one while on the island, and then never formally broke things off with her, just kind of left her by the wayside while he turned his sights to Josette. Of course, to assume that Barnabas used Angelique at all would be kind of going against his character because he was being portrayed on the show as morally righteous. Then again, he did kill his Uncle, who was raised as his brother and was his best friend. So, shit happens I guess.
It is possible, as Sunny Collins said, that maybe Barnabas had the tryst with Angelique to go against his domineering father. I'm not sure that's what he really did. It's kind of hard for me to believe that Barnabas would take such a radical action, given the rational guy he was before he was turned into a vampire. But young people do stupid things, and Barnabas is no different. There's no telling what he did before we saw him in 1795. I mean, didn't he say that he lusted after Laura Collins, Jeremiah's first wife, when telling Sandor the story of Laura in 1897? So if he lusted after her, then there was definitely sin in his heart as defined by biblical terms and what many people believe.
For me personally, I like to believe that Barnabas and Angelique had a fling, that he dropped her when he caught sight of Josette, her mistress, and that's how Angelique's scornful ways began. Because basically what Barnabas did, if he did do that, was tell Angelique that he wasn't good enough for him because she wasn't rich and wasn't the daughter of a respectable man. If that's not a big slap in the face, I don't know what is.