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They need to be kept moist, but not wet. It may just need water. You can use an organic soil or one that is slightly acidic. Add crushed lava rock to aid drainage. A plastic pot will be easier to manage at the plant grows. When it becomes rootbound, transplant into a pot one inch wider than the previous pot.

Here are care instructions:
https://www.gardeningknowhow.com/houseplants/coffee/growing-coffee-plants-indoors.htm
https://www.gardeningknowhow.com/houseplants/coffee/pruning-coffee-plants-indoors.htm

The problem with all of the genus, Phoma, is that they are all very resistant to fungicides, or any treatment for that matter.

The best defense, going forward, will be prevention. This will come down to keeping all leaf litter and plant material off of the surface of the soil, mostly. Pair this with watering ONLY when the soil is completely dry ,down to about halfway, the container and you may beat this.

One defense that I will recommend is something that I use for my citrus when they contract hard-to-rid infections is a casting of 1/2 cup DOLOMITIC LIME and about a Tablespoon of WETTABLE SULFUR per tree, around the soil.

This can make the soil very unfavorable to fungi and quite favorable for the tree, while providing a few of the lesser nutrients- Like Carbon, Oxygen, Sulfur, Calcium, and Magnesium.

Here is an article for more information on Phoma: https://www.gardeningknowhow.com/plant-problems/disease/phoma-blight-disease.htm

Here's an article that should help answer your question.

https://www.gardeningknowhow.com/houseplants/coffee/pruning-coffee-plants-indoors.htm

Your plants that are shaded may not be getting enough sunlight, or perhaps they're not draining well. Your soil should have a pH of 4.2 to 6.0. If the plants in the sun are doing well and the others are not, that may be the answer to your question. If you think there's something more critical, you may want to contact your local agricultural extension service for more help. Here's a link:
https://www.gardeningknowhow.com/extension-search?zip=91001&radius=20&services_search_action=search&submit=Search

https://www.gardeningknowhow.com/ornamental/shrubs/coffeeberry/growing-coffeeberries.htm

Back off on the water and the fertilizer and it should be fine. (Fertilize every two to three months in spring and summer). Here are tips on how to grow coffee plants:

https://www.gardeningknowhow.com/houseplants/coffee/growing-coffee-plants-indoors.htm

You could move it to one size larger container but plant it at the same level it was in the first pot. Covering up the stem with soil could lead to stem rot. You can pinch off the top two leaves to get it to branch more.