2 recurring issues I see are dampening off and root rot
Root rot can be addressed by adding a water chiller. If your water is above 70-75 F you should absolutely be using hydroguard.
The cocoa pods are WAY too low for most of the pics.I have looked at. That pod should only ever be wet when the seed is germinating. After that, until the roots are formed after about 3 weeks, the majority of moisture is absorbed by the leaves through humidity (therefore RH should be around 70-80%).
To help the dampening off, try squeezing as much water out of the pod, raise it as high as you can because the thing is basically an organic sponge. Roots should start out barely even being sprayed with the bubbles from the air stone. The pod should NOT.
Also the more air you can get to the bas.of the stem, the better.
If the pod is wet, with no air, the plant “thinks” it’s needs roots there, and starts developing them above that point. This causes the plant to thin out and become pliable and eventually kills the plant. It is essential to get air on the base of the stalk.
Also Silica such as Armor Si will help bulk the firm parts of the plant and resist disease.
A little research goes a very long way with these ladies.