Ants, by themselves, are weak creatures, but
when ants are considered along with others of their species, they are known for their highly organized and powerful colonies and nests, which sometimes consist of millions of individuals.
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A. when ants are considered along with others of their species,
no issues, keep.
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B. when considering them with others of their species, then
considering them with others of their species is too wordy and grammatically incorrect to use "when considering them with other..."
the "then" here is redundant.
who is them / their referring to? ants or weak creatures?
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C. ants, when considered with others of their species,
here "their" is NOT an issue as we have a clear referent "ants". the issue is the construction.
as explained by another user above "remove non-essential modifier "when considered with others of their species", we have "ants they are known""
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D. considering them with others of their species,
same issue as B
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E. considered with others of their species, then
issues as discussed above.