Mods are constantly in conflict with Vanilla, and each other. Minecraft mods override base functionality. Other mods might also override that same base functionality. This potentially makes them incompatible, or cause crashes when vanilla Minecraft expects a particular value but gets another.
This is a problem whether or not modders list their incompatibilities with other mods - because if two things exist then someone, somewhere, someday will find an excuse to try and put them together. And it's up to us to know about every mods incompatibilities (or know how/where to find a list of them, if it exists).