I've noticed it with some of the extracts and tinctures -- especially the tinctures, which I attribute to the alcohol content. I think the cellulose content of the kratom might be what's bothering you. I've noticed eating apples and other raw fruit/veg I sometimes get very bad heartburn. I've been told it's because your stomach gets very acidic in an effort to break down cellulose.
I find that drinking antacid solution helps. If you can find it, Alka-Seltzer Heartburn Relief is great. I don't know why it's become difficult to find, but they should have it on Amazon. It's an antacid only, so no aspirin or other medications like in the other Alka-Seltzer types.
One thing I have noticed though, if I take acid reducing pills like Prevacid or Pepcid, I seem to have a greater likelihood of experiencing the unpleasant kratom side effects (headache and hangover type symptoms). I don't know if this is a direct interaction, or a consequence of reduced stomach acid.
Thank you! I will give that a try.