Two past perfect verbs in the same sentence even though sequence is indicated

A group of environmentalists helped direct several small sharks that had lost their way after they had swum through polluted waters to migrate South.

Swimming comes before losing the way, yet both verbs are in past perfect. I'm told that this sentence is correct. Is this sentence correct and what about the past perfect should I know to explain this usage?

It is correct. Both actions happened before the fact that the environmentalists helped the small sharks, that's why they need the Past Perfect form. The use of after specifies which of these two actions happened first, i.e. first the sharks swam through polluted waters, then they lost their way.