Zoo keepers not cleaning habitats?

I don't know where to put this. But I'm having trouble getting my keepers to fully clean my saltwater croc and tapir habitat. It looks like there's poo in the water and when I remove the animals the habitat goes to 100% clean and then when I put them back it goes down to where I'm getting notifications saying they are a disease risk. How do I fix it?
 
When the keepers is cleaning, box the animals and remove the water for a moment.
When he cleaned it, put everything back.
Its a known poo-in-the-water-issue they're working on (i hope ^^)

There can also be poo below a shelter with a bottom, delete the bottom or use another shelter without a bottom to prevent that.
 
My zoo has gone into meltdown, when removing water and shelters I can see it underneath. currently have 6 exhibits but the 2 quarantine stations are full and there is a long queue at both vets clinic.

For the moment I am going back to doing some landscaping, or trying anyway, as I am sure it won't be too long before it's rectified.
 
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