Your sand looks fine. The brown stuff could be diatoms, which usually go away soon in a new tank. You could try siphoning any detritus (grey organic particles) from the sand. Using airline tubing (used with aquarium air pumps) can be helpful in minimizing how much water is also siphoned during the process.
Some additional tips:
Your clown is either Amphiprion ocellaris or A. percula, and clowns are also part of the damselfish family. Damsels are normally aggressive, as your four stripe damsel (Dascyllus aruanusshows in the video when it attacks the clown, but ocellaris/percula clowns are unique for being relatively peaceful. It's a good idea to remove the damsel if you want to add more passive fish.
It's odd that a peppermint should attack a healthy hermit. Maybe the hermit was molting its shell and thus vulnerable. Also, having only one turbo snail and a hermit (or soon to be no hermit) is kind of small for a clean up crew. See my second link for a great guide to more clean up crew animals.
The aiptasia anemones in your tank are really huge. Peppermints can be hit or miss with aiptasia removal, and sometimes the larger anemones remain untouched. Search my first link for other aiptasia removal methods.
I strongly suggest checking nano-reef.com, which is a forum devoted to small tanks like your biocube. One of the most useful subforums there would be the all-in-one tank forum, which has the "biocube resource thread". This thread is really useful in giving tips on modifications for your tank. For example, the biocube skimmer is not very effective, and many people take it out to make use of its compartment for other purposes. Likewise, it looks like you have the stock filter media, which could be trapping detritus and becoming a nitrate factory. This could in turn be a cause for algae problems on the sand bed.
Good luck with your tank!