If you are unable to use your Sub Skill Seed, it is possible there are no available sub skills that can be used with the seed.
One possibility is that you have two overlapping skills with different rarities. For example, if you have a ""Skill Level Up S"" and a ""Skill Level Up M,"" you cannot raise the ""Skill Level Up S"" to a ""Skill Level Up M.""
Or, the sub skill may be at max rarity. Depending on the sub skill, there are three maximum rarities: S, M, and L. It's important to note that not all sub skills have a max rarity of L, or a rarity to begin with.