I hope this is a display error only.
The Skill window shows inconsistencies on which skills enhance Plasma, Transphasic and Tricobalt mines. They are consistent in that Starship Projectile Weapons Training and Starship Mines enhance all of them, but all are enhanced by Starship Photon Projectiles (?)

Plasma Mine:
Starship Torpedo Weapons (<-listed but should not enhance) | Starship Photon Projectiles (?) | Starship Plasma Projectiles

Transphasic Mine:
Starship Photon Projectiles (?) | X *Missing Starship Transphasic Projectiles X

Tricobalt Device (mine):
Starship Photon Projectiles (?) | X *Missing Starship Tricobalt Projectiles X

Ticket ID# 857,290

I haven't checked other mine types. (Edit: Tested other types; see following post)

Additional Mine types which are not getting bonuses from their specific skills:

Quantum Mine:
Starship Photon Projectiles (?) | X *Missing Starship Quantum Projectiles X

Chroniton Mine:
Starship Photon Projectiles (?) | X *Missing Starship Chroniton Projectiles X

The only mines that appear to be getting skill bonuses properly are Photon Mines.
Plasma mines are getting an extra buff from Starship Torpedo weapons, and the rest of the mine types are missing their specific Projectile Type skill enhancements but all types are flagged to get bonuses from Photon Projectiles.