Can one say
a. I ate apples in the fridge.
b. I ate apples that were in the fridge.
I don't know why (a) sounds to me as if I was in the fridge when I ate the apples. "In the fridge" seems to be adverbial and not adjectival.
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"I ate apples in the fridge" sounds like you were inside the fridge when you ate them!
You could say:
-I ate the apples that were in the fridge.
-I ate the apples from the fridge.
Although the latter could also sound like you stood at the fridge and ate them straight out of the fridge (like you would say "I drank my coffee from the mug").
Having said all that, eliminating ambiguity is not essential to speak English - a native speaker might well say any of the above, including your examples, and most people would not pick up on the ambiguity.