This is loaded question IMO. Flow is very important for one and of course water changes, not over feeding and a good light schedule to name a few.
I have a bio cube also and it's now a little over a year old, no issues (knock on wood)
I can only speak based on my experience and practices.
I have the inTank media rack, I use to have the skimmer, I think the skimmer for the bio cube a waste of money and I'll explain why. I had one like I mentioned. You need to keep the water level at a consistent level which is impossible in chamber 2 where you have to put the Tunze 9002, because that water evaporates everyday and you'll notice the the level dropping. Once it drops your skimmer will not work properly and you'll have to constantly dial it in. I was doing this almost twice a day!
Since then I've gotten rid of the skimmer and just placed live rock rubble in chamber 2 along side the media rack. I run purigen, phosguard and chemi pure elite. I also change my poly floss/filter floss 2x's a week and test regularly.
I do 5 gallon water changes every Saturday.
I mentioned flow before. Low is important in keeping the water clean and clear. Too little flow and you won't kick debris around and allow for the filter intake to get it. I run a upgraded pump the Maxijet 1200 and 1 mp10 Vortech set on 60%
You also want to agitate the surface an from your pictures the outtake and power heads are pointing downward or not at the surface. One should be pointing upwards IMHO.
What type of power are you running? Have you checked for phosphates?
What's your water changing schedule like?
Here's my tank after 1 year
I run a single AI SOL BLUE LED fixture cut into the stock hood.
Also I forgot to ask... Are you using any chems? Phyto etc? This can also play a factor into many issues.