Well, these are utility items, so they wouldn't show up as Secondaries anyways (except on Grenadiers, iirc).

Is odd they're not showing up in utility items. should be right by grenades (and Molotovs and pipe bombs if you use those mods).

In my case they even appear, but I can't put them in any slots.

When I put it, it doesn't let me put anything or take the previous item out of the slot, only leaving this "bug" when I leave the soldier's "arsenal" screen and pass the bug to.

How could I fix this?

so if you guys are having issues with the utility slots, try removing every utility item on your soldier and then check the first box. For some reason it doesn't show up when multiple utlity slots are filled and it locks you out of the second one for me

Yeah I'm experiencing this as well except for the proficiency class's Sapper as a secondary
though I'm not sure if this is also from Shiremct's Weapon and Item Overhaul or Iridar's True Utility Slot Sidearms

Well found a way to fix it!
it has it's own mod menu in which you can set it to whatever slot you can equip it to
for me I set it to grenades and not take up two slots and it worked!