Conflicts in the configuration - If multiple modules depend on the same module this can cause a conflict. To resolve this you would need to have one module keep the dependance the same and the second module would need to depend on the first module.
Rewrite conflicts - A conflict can happen if two classes have a rewrite of the same class. The way to resolve this is to merge the code of the two rewrites into one class and then make the new class the rewrite.
Conflicts in the theme - A conflict can happen in the block layout files. This could be two blocks using the same name or two layout files manipulating the same block. To resolve this you can check block templates and types using the template hints.