Well...if it were me I would say the apples. I cannot eat them without getting indigestion. ugh.
Here's my story if any of it might help you figure it out.
Diagnosed "probably celiac", based on blood work that was "suspicious". I didn't question her too much because by then I'd gone off gluten and felt 200% better. I didn't care to do the gluten challenge in order to have an endoscopy because I don't care that I don't have an "official" label. All I knew was that I felt better.
I went off gluten and ate everything else. Lots of corn, of course, because of corn chex and corn tortillas etc. Fast forward to about six months ago. Suddenly I realized that much of the time I had terrible indigestion and often bloating after eating. I was SURE there was no gluten in anything I'd eaten because when I've done the cooking and it's chicken and potatoes and green beans....well, there's no gluten.
I began to wonder if it was the corn, or other grains. So, as an experiment I went off of all grains. And wow, felt 200% better again! My plan had been to add them back in one at a time so I could see which one it was. But almost before I could do that I had an appointment scheduled with my doctor for a regular checkup. And to my surprise my blood work showed an elevated a1c, which indicates what she called "pre-diabetes". Her prescription was to lose weight, exercise and cut down on carbs. NOT no-carb which she said is not healthy (in her opinion).
She recommended a nutritionist, and two books: "The Glycemic Load Diabetes Solution" by Rob Thompson, MD, and "The Insulin Resistance Diet" by Cheryle R. Hart, MD, and Mary Kay Grossman, RD. The nutritionist also said that both were good basic info about carb-protein "linking". Basically you have to not have a lot of carbs all at once, and what you do have you need to eat with protein. So my breakfast of coffee and two slices of Udis with butter and jelly, followed by Corn Chex with fruit and milk was just about the worst thing I could eat. That explained my sudden ravenous hunger and shakiness mid-morning. ugh
So now my breakfast might be one piece of toast with an egg, or cheese and sliced turkey, or cottage cheese with a small amount of fruit, and maybe some almonds. And no apples, because fruit is carbohydrates and for some reason apples upset my stomach. That breakfast holds me till lunchtime! And at lunch I'm just ordinary hungry, not ravenous must-eat-everything-in-sight-especially-bread-with-butter hungry. lol
My doctor said that indigestion can be a sign of pre-diabetes and that explains why I felt so much better when I cut out grains. Also I had been eating a lot of potatoes since I figured they're gluten free and bland for my stomach. Nope, they may be bland but they're carbs.
So basically I've given up all "white" and "processed" carbs. I still eat fruit, but not a HUGE smoothie worth of it first thing in the morning. I still put some sugar in my coffee -- I like the sweetened creamers and I'm not messing with my coffee. Priorities you know. lol.
So those are my experiences, and maybe something in there might strike a cord for your situation. I know how frustrating it is to still have uncomfortable symptoms and not know what's causing it!