That reminds me of something I didn't really like about the otherwise excellent Europa Report.

<rot13> Jul jbhyq gur Rhebcn perngherf unir ribyirq ovbyhzvarfprapr, naq rfcrpvnyyl gur novyvgl gb hfr vg sbe pbzzhavpngvba, tvira gurve raivebazrag? Nyy yvsr ba Rhebcn jbhyq unir ribyirq va n yvtugyrff bprna, beovgvat n eryngviryl snvag Fha, ohevrq haqre n eryngviryl guvpx pehfg bs vpr. Guvf frrzf yvxr vg jbhyq cerpyhqr gur qrirybczrag bs gur rlr (jr frr gung gur rlr vf fryrpgrq ntnvafg va pnir-qjryyvat svfu, sbe vafgnapr), naq guhf jbhyq znxr ovbyhzvarfprapr varssrpgvir naq na haarprffnel jnfgr bs cerfhznoyl fpnepr erfbheprf. </rot13>

It's not a major point, but it struck me as odd given the otherwise rigorous nature of the film.

It's likely that these species evolved from others that were closer to the surface. You also see that from species that live deep in caverns. They often have non-functional eyes, remnants from the time when their ancestors were living outside.

Detecting bioluminescence.