Yep.
There's also a learning limitation if you equip one character with two Enemy Skill Materia.
Let's say that Cloud has an empty ES Materia and an ES Materia with Matra Magic. If you go into battle and an enemy uses Matra Magic against you, the empty Materia will not learn Matra Magic.
However, if an enemy then uses, say, Flamethrower on Cloud, both Materia will learn it.