Take another look at the original sentence:

Susan ducked down when she saw Mr. Hayden, her English teacher, walk into Tito's Taco Palace, unfortunately, a burrito wasn't big enough to hide behind, so poor Susan had to explain why she had missed his class again.

You chose to fix it the correct way:

Susan ducked down when she saw Mr. Hayden, her English teacher, walk into Tito's Taco Palace. Unfortunately, a burrito wasn't big enough to hide behind, so poor Susan had to explain why she had missed his class again.

Susan ducked down ... begins a complete sentence. Unfortunately, a burrito wasn't big enough ... starts the next sentence. You are always correct when you use a period and a capital letter between the two sentences that create a comma splice.

Go to the next sentence.

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