Hmm.
I recall someone having a similar issue to this a long time ago that I'd thought I'd fixed. It revolved around the fact that his ingredient items weren't independent items (from the YEP_ItemCore), and a weird interaction with the way my plugin was adding traits together. It's possible the fix I implemented didn't take the second (or third or fourth) ingredients into account when doing whatever it was I made it do to fix the problem.
One question, though, are you using the YEP_ItemCore plugin to make your ingredients independent items? The problem I mentioned above was actually because the user wasn't using the ItemCore at all, and while that is okay, the additive traits were never intended to work in projects that didn't have that.