Minecraft: 1.12.2
Forge: 14.23.5.2838

Mods: 4
jei_1.12.2-4.15.0.279
Mantle-1.12-1.3.3.55
TConstruct-1.12.2-2.12.0.157
yoyos_1.12.2-1.3.3.24

Unsure if it's 'Tinkers Construct' or 'Yoyos' so I'll give it a mention here first.

I noticed this when attempting to emboss a Prismarine Body onto my yoyo so it'll have the traits "Jagged + Aquadynamic"... however... apparently only the "Aquadynamic" trait from that material gets embossed onto it. If I add the body material to replace a body material, I'll get those traits normally.

I tried other materials that gives two or more traits... such as Yoyo Bodies and apparently those are affected as well. Just to name some materials and going by just the mods above...

Netherack Body - Aridiculous + Hellish
Grants "Hellish" if embossed.

Pig Iron Body - Baconlicious + Tasty.
Grants "Tasty" if embossed.

Knightslime Body - Sticky + Crumbling.
Grants "Sticky" if embossed.

If going by extra materials added from other mods, such as Plustic + others...

Plustic + Draconic Evolution
Awaken Body - Rude Awakening + Brown Magic.
Grants "Blind Bandit, Apocalypse & Global Traveler" if embossed.

Plustic + Armorplus
Guardian Scale Body - Divine Shield
Grants "Aquadynamic" if embossed.

Axles & Cords seems to emboss correctly as far as I can tell.

P.S.
Now this one I am not sure if it's Plustic or Yoyos. Some materials aren't available as usable parts for the Yoyos. One example is 'Bloodwood' which is missing for Yoyos but Fusewood, Darkwood & Ghostwood Yoyo parts exist for them if you have Natura added.

I would like to add that another broken Embossment is with the End Stone body part, the body is intended to give the Alien trait, but if you Emboss it, it gives Enderference (which is given by the axle part)