Option B — Error: ate / Correction: eats
The sentence describes a habitual action ("usually"), so the simple present tense eats is correct throughout.
When a sentence describes a habitual/routine action (signalled by "usually"), both verbs must be in simple present tense. "He usually eats breakfast before he goes to school" — but since goes is already present tense and correct, only ate (past tense) is the error. Option D is wrong because changing goes to went would make both verbs past tense unnecessarily; the sentence needs present tense, not past.