WGCNA module preservation analysis
Your question is not clear, you seem to mix the relevant terminology... 

First, you cannot run WGCNA for individual samples, only for individual conditions (with or without WT, depending on what question you're trying to answer and assuming you have enough samples in each condition). If that's what you have done, fine. The number of modules in each independent analysis will generally be different, that's because each condition is different. The module identification built into WGCNA as the default approach does not allow the user to specify the number of modules beforehand, but if you insist on getting a pre-specified number of modules, you could run WGCNA using the "manual" way (for example, Tutorial I, section 2b) and substitute another clustering method (e.g., PAM) that allows you to specify the number of clusters. You may find the results inferior though.

Second, module preservation does not result in new modules. Module preservation evaluates whether modules found in data set A are preserved in a different data set B. To get new, common modules, you could run a consensus network analysis on pairs of conditions or all 3 conditions together. The number of modules you would find in a consensus analysis cannot be predicted from the number of modules you find in individual data sets.