You usually let the pot of jelly sit for 5 min. Stir and as it cools a bit the peppers or other fruits in jam will mingle in with the jelly part. It is because the peppers are lighter than the syrupy part.
Not sure you can do it now until you open it and stir it in.

Agree it was likely jarred too soon. Wife is still fighting this problem after 4 years of making this and she mutters every time.

You can 'try' inverting the jars once the seals have set (leave the bands on). Sometimes that will let some of the fruit disperse up through the jelly. But it can also cost you your seal.

The best method is to just stir the jar contents well after opening. That's what we do.

Next time heat the peppers longer to force more of the air out of them and then as Linda Lou said let it cool some and carefully stir it before putting in the jars. Good luck.

Dave

Thanks for the tips, glad to know its not just me.