Even if you click the 'Mark as brewed' button the appropriate number of times, there are some other potential problems that can bite you if you're not careful.
Several times, the 'Mark as brewed' button gave me fits because it thought I didn't have the ingredients in the recipe on hand. Usually it's because I had slightly different varieties specified, like 'Hallertauer Mittelfrueh' in recipe vs. 'Hallertauer' in inventory, or 'Pilsner (Weyermann)' in inventory instead of 'Pilsner (2 row) Ger'. When Beersmith complains that I don't have enough of an ingredient in stock, I'm never sure if it correctly decreased the amounts of the other ingredients, and I have to manually adjust what was actually in inventory. After hitting that problem about three times in two months, I gave up using the inventory feature.