A: Are you sure they're the enemy?
B: They shot at me./They were shooting at me.
Are these interchangeable in every way?
Are they equally natural in the context?
If it was repeated firing, would the past continuous be more natural?
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To answer your question, we would require more context.
It's not clear whether the shooting refers to a single shot or a series of shots/volleys over a period of time.
If they just shot at you, the implication is either a single shot or several shots in quick succession. But this remains uncertain.
If they were shooting at you, the implication is of a more prolonged attack and the past continuous would fit the context better.