It seems that JAOPCA when adding Netherite Scrap Dust recipe to the Integrated Dynamics squeezers (integrateddynamics:squeezer and integrateddynamics:mechanical_squeezer), it sets an input tag of c:ores/netherite_scrap instead of c:ingots/netherite_scrap.
Ancient Debris has the tag c:ores/netherite_scrap, while Netherite Scrap has the tag c:ingots/netherite_scrap.

This causes the dust creation to come from Ancient Debris, instead of Netherite Scrap like normally intended and this a duplicate recipe for it:

It's normally supposed to be Ancient Debris => Netherite Scrap => Netherite Scrap Dust, every other mod recipe seems to follow that. This also makes the ID native Ancient Debris => Netherite Scrap squeezing sometimes be overridden if the JAOPCA entry happens to be above it in priority (this is the case for mechanical squeezer, so there dust is being created instead, and in regular squeezer it's scrap).

It seems these two recipes are what's causing the issue (exported via Crafttweaker):
<recipetype:integrateddynamics:squeezer>.addJsonRecipe("jaopca:integrateddynamics.ore_to_dust.netherite_scrap", {type: "integrateddynamics:squeezer", output_items: [{item: {count: 1, id: "occultism:netherite_scrap_dust"}}, {item: {count: 1, id: "occultism:netherite_scrap_dust"}, chance: 0.75}], input_item: {tag: "c:ores/netherite_scrap"}});
and
<recipetype:integrateddynamics:mechanical_squeezer>.addJsonRecipe("jaopca:integrateddynamics.ore_to_dust_mechanical.netherite_scrap", {output_items: [{item: {count: 2, id: "occultism:netherite_scrap_dust"}}, {item: {count: 1, id: "occultism:netherite_scrap_dust"}, chance: 0.5}], duration: 40, input_item: {tag: "c:ores/netherite_scrap"}, type: "integrateddynamics:mechanical_squeezer"});

I think this'd be fixed if the jaopca:integrateddynamics.ore_to_dust.netherite_scrap and jaopca:integrateddynamics.ore_to_dust_mechanical.netherite_scrap recipes would take c:ingots/netherite_scrap as input, instead of the current c:ores/netherite_scrap.

This is tested with a clean 1.21.1 NeoForge (21.1.208) instance with only the bare minimum relevant mods present (ID + JAOPCA + JEI and dependencies):

architectury-13.0.8-neoforge
commoncapabilities-1.21.1-neoforge-2.9.12
cyclopscore-1.21.1-neoforge-1.26.2-808
integrateddynamics-1.21.1-neoforge-1.27.9-1308
JAOPCA-1.21.1-5.0.12.18
jei-1.21.1-neoforge-19.22.1.316

should be fixed