There is at least one way that this can happen:
let's say that some settings of the mod A rely on a group of settings in another file, be them stock settings or settings from a second mod (B) that the said mod A is based on. The author of A, assumes that the essential settings are already in game, and he doesn't include in his package the files containing them.
A third mod, let's call it C, might remove/change the aforementioned settings. Note that, though conflicting with B, C might be designed to work well with the latter. Nonetheless it doesn't take into account A. result: despite the fact that it is not overwriting any of its files, C will break A
There are also cases where a mod can mask an incompatibility between two other mods. A practical example: in sobers' mega mod, OHII follows FXU. Their relative order didn't matter before FXU 0.0.22, because their conflicting files were identical, but now some new settings which were added to FXU are not present in OH. This is not a big problem anyway, because RSD, which is enabled on top of them, ovewrites the two mods, restoring the missing settings. But try removing RSD without switching OH's and FXU's relative orders, and you will transform a stable mod list into a buggy one.
