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I've seen this occur in my own garden; twins happen! It will not effect your plant or the production of fruit.

6" x 3"? No. Only suitable for a single small plant,
6' x 3' then Yes for the three tomato plants in one, one or two pole bean poles and two to four cucumbers that can cascade over and trail outside the box.
The better you prepare the soil with compostand mineralized complete organic fertilizer, the more intensely you can plant the beds with nutrition for all. And good water management is important too.

A single cucumber will require a VERY large container indoors, as well as horticultural grade lighting. You will not be able to provide enough through the window to even keep it alive, much less getting it to fruit.

You will have to grow each of these in a container that is at least 2 gallons each. They will need about 100 watts per square foot of lighting of some sort as well.

Can you include photos of the area, the plants, containers that you intend to use, and any other useful photos? This will give me an idea of the space that you have to work with, the amount of light that they are receiving and just to see the plants. This can give me a better idea of what I can recommend to get them looking better.

What is the soil type that these are growing in? Are the parts that are affected close to the light? It almost looks like sunburn. Not from heat, but intensity. I run LED myself, and this problem is common when they get too close to the light.

Anthracnose is a fungal pathogen occurring in moist, warm conditions. The first symptoms to appear are circular yellowish spots that turn brown to possibly reddish. The fungal disease may cause all the leaves to have a burned-out appearance and sunken spots develop on the fruit with a pink-colored substance seeping from the spots. Brownish black streaks may also appear on the stems of the plants. Splashing water -- from rain or irrigation -- will spread this contagious disease from one cucumber plant to another. Once anthracnose is established, it is difficult to control. Fungicides will control this fungal disease if applied at the first sign of infection.
https://www.gardeningknowhow.com/garden-how-to/info/using-fungicides-in-garden.htm

This article may be of interest to you:

https://www.gardeningknowhow.com/edible/fruits/cassabanana/grow-cassabanana-plants.htm