No system in full proof. It’s always best to know what exactly you’re downloading and if your mods conflict with other mods by reading what the creator wrote in their description. The mod conflict program will not tell you which mods conflict. Don’t load a lot of new cc and mods in at once. In case you have issues, it is easier to find the culprit through a process of elimination. I write a better longer tut on how to look for bad cc in the future, but this is just a quick PSA.
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Just an FYI for using Mods. When you download mods, ALWAYS read the creator notes for information that may conflict with other mods, resources used that could conflict, etc. The Mod Conflict app will not tell you what mods are conflicting in your game. Therefore it is best to know exactly what you are downloading and what you already have in your game. Mods that change/enhance gameplay can be a lot of fun, but they are powerful tools and if you choose to use them, take precautions and know what you’re doing. Also deleting Last Exceptions (LE) won’t make your problem go away. Happy Simming.