Yes, insect larvae can be associated with damage to exposed EPDM pond liner in some circumstances. The source example describes caddisfly larvae and marks in a bare-liner pond. That is a specific observation, not proof that insects caused every mark you might see on a liner, and not a general explanation for a falling water level.
What does the example actually show?
The reported damage occurred where the liner was exposed. Caddisflies spend a larval stage in water, so an insect-related mark is plausible in that setting. A photograph or a surface mark alone does not establish when the mark formed, whether it goes through the liner, or what caused it. This article does not offer an identification test for larvae or a way to confirm a leak from the appearance of a mark.
What should you note if you see a suspicious area?
Record the location and take a clear photo without pulling or cutting the liner. Note whether the surface is exposed and whether you have actually observed larvae at that spot. Keep observations separate from conclusions: a visible scratch, shallow mark, and puncture are not the same finding. If you suspect a leak or need a repair, seek advice for your particular liner and pond setup rather than choosing a repair method based on an assumed insect cause.
Keep the question in perspective
EPDM is one part of the pond's construction. For a broader overview of choosing pond components, see The Ultimate Guide to Essential Koi Pond “Must Haves” for Beginners. That guide does not diagnose insect damage either.
The useful takeaway is narrow: insect larvae are one possible consideration on exposed liner, but the marks and their cause must be assessed on the actual pond. Do not treat a suspected insect mark as proof of a puncture or as an explanation for water loss without further inspection.