Thanks! Are you using dried tomatoes that come in olive oil? If so you may need to get some of the moisture out either by patting dry or letting them sit in flour first. When I use jalapeños in my bread I let them sit in flour for a few minutes before incorporating into the dough so they don’t make mushy spots.

When you use them on top, are you tenting your bread with foil at a certain point while it’s in the oven? That should help keep the top from burning.