It depends on the type of conflict. If you use BAIN to install mods I believe you can use it to identify resource conflicts, e.g. if two BAIN packages install the same texture file and would overwrite each other, Wrye Bash will tell you that,
If you're talking about conflicts within the ESP themselves - I'm not aware of Wrye Bash having a conflict detector of that type. However, TES4EDIT does a great job for detecting conflicts within your load order. On caveat, however, if you use the "ghost" feature in Wrye Bash to hide the ESP files that are being imported and are therefore inactive, TES4EDIT won't detect them. Files need to have a .esp or .esm file extension.