As you run more, your body may adapt to having food in your tummy, too. After running a lot, I can eat different foods before running than I can when I spend weeks not running at all, and closer to the time when I start running. So, don't despair too much that it's a permanent or difficult affliction.

It may be the amount of time between when you eat and when you run, it might be the high fiber/sugar foods. Maybe switch to a banana instead of an apple, or try adding the protein (I usually try to pair a little protein with carbs in a snack anyway).

Running is definitely harder on the tummy than riding - though if I go out and do hard intervals, hills, or sustained higher intensity in any way on the bike, it feels a lot more like running than a nice smooth commute or afternoon ride.