Planting deep isn't the problem. Over watering is always bad, but several things can cause brown plants, including diseases and fungus. Search around this forum for discussions and photos, and I'm sure others will post more.

causing my plants to turn brown

Need more details or a picture of the plants if possible as "brown plants" is too vague. There are many possible causes of plant problems - bad soil, too much fertilizer, disease, wind/sun burn, too much water, pests, etc.

But deep transplanting is standard so that isn't the cause of the problem unless the main stem got broken in the process.

Dave