Most of these conflicts are due to the fact that the modder copied/duplicated items from another game cell into their own. As a result Creation kit marks the cell as "modified" and therefore saves it to their mod often unbeknownst to the author of the mod.
Here are my thoughts on the matter.
1) This aspect of the creation kit needs to get more attention so everyone knows about it... perhaps put into the introductory Mod Tutorials so that new modders are aware of how their "copy & Paste" effects their mod and can potentially cause unintentional conflicts.
2) There needs to be a way to "reset" a modified cell back to normal. Forgive my ignorance if there already is a feature in the creation kit to do this but I have been modding in CK for 4 months now and I have yet to find it. And Yes I realize you can create a new clean mod and paste your modded cell into in order to "clean it" But lets face it that's a pain in the butt and there should be an easier way.
3) I am asking, begging, pleading and entreating that Bethesda releases an update that adds this functionality to the creation kit as I feel it will truly improve the quality and compatibility of the mods coming out of the modding community.
4) If you agree with all of this please comment below, bump or in some way show your interest or support of this idea so that it gets enough traction that bethesda will notice it.
Best Wishes and happy modding
Sku11M0nkey.

