If the joints are LESS than ¼” – don’t fill the joints w/ mortar (it will just fall out).
If the joints are LARGER than ¼” – go ahead and fill them in w/ high-temp mortar BEFORE you fire your oven. If you fire the oven, it will create soot / smoke and leave a film on the brick… which will prevent the fresh mortar from attaching to hard mortar in the oven.
If the mortar patch ever falls out AFTER you fire the oven, scrub the area with a metal brush, and then apply Rutland 10.3oz high-temp mortar from a tube –