Hola Emanuel

In this sentence:

El chocolate que te comiste era mío. (The chocolate (that) you ate was mine.)

"te" is not the subject of the sentence. Te is the reflexive pronoun used sometimes with verb "comer" -> "comerse". When we use reflexive pronouns with verb comer, we give emphasis to the action. 

You can add subject "Tú" to the sentence if you want:

El chocolate que tú te comiste era mío. (The chocolate (that) you ate was mine.)

This is absolutely fine as well. But, remember, in Spanish we tend to omit subject pronouns, as we know who the subject of the sentence is by looking at the ending of the verb. 

Un saludo cordial

Inma