Hello!
- "SCP-5378 is the designation for two sentient/sapient ladybird beetles,1 which are referred to as SCP-5378-A and SCP-5378-B." — You can just say 'sapient' (sapient implies sentient). I'd also make this much simpler: "SCP-5378 refers to two sapient ladybird beetles (SCP-5378-A and SCP-5378-B)."
- "Both SCP-5378-A and SCP-5378-B were capable of constructing miniaturized versions of manmade structures/objects using natural materials, such as leaves, rocks, and dirt." — "Both instances constructed miniaturized versions of manmade structures and objects using materials such as leaves, rocks, and dirt."
- 'A small tent made out of leaves.' — I feel like you can make this much more adorable by digging in deeper. Something like 'A small tent comprised of two propped up holly leaves', or something. Something that immediately gives us a clear, specific, and fragile image.
- 'A sleeping bag within the tent.' — Again, I feel like just a tiny detail (what was the sleeping bag made of?) would emphasize the adorableness, here. Something like 'A sleeping bag made of loose twine', or 'A sleeping bag woven from feather down from a dove'.
- 'Two separate sleeping bags.' — I'd change this to 'A second separate sleeping bag', unless they actually made two more (thus ending up with three).
- 'A letter.' — 'An envelope carved from a robin's shell' or something equally adorable.
- 'A bench.' — 'A bench constructed from a toadstool'?
Overall, I liked this piece; the ending was sweet, even if the final note was a smidge maudlin. I think it might be a bit stronger if you emphasize the materials used to create that sense of 1) fragility, and 2) adorableness — particularly adorableness, because of how that adorableness contrasts with the gravitas of the final note. Convince us to see their 'lover's dispute' as just an adorable opportunity to admire their furniture, and that final note becomes much more powerful (because we're not ready for the adorableness to shift into sadness).
In particular, I'd also change the letter to an envelope to throw the reader off the scent of what's coming — letting the reader think the envelope is just a prop with nothing in it, but then revealing that researchers examined it and discovered it contained an actual letter they could read with a microscope.
I think you might also get something out of (lightly) emphasizing the amount of time passing here (maybe another heading?) — the idea that this whole drama occurs within just a few months is particularly fun (and charming).
Either way, even without any of these changes, I found this charming. Good luck with the article!