I believe it is not the condition but the number of replicates that are required for running WGCNA. Typically, you are required to have more than 15 samples. Ideally, I would recommend more than 30 replicates for each condition.
Here is the list of frequently asked questions: https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/faq.html
Another advice would be plotting PCA/MDS plots to check if there are no Batch Effects or technical effects such as sex, non-biologicals effects.