I did not track these, I am only reporting on them:
1) Necessities of Morrowind v2.13:
Fountain activators (specifically Balmora Temple) were changed and NoM no longer recognized them for drinking or filling containers. Since this was reported, _Taddeus_ has fixed it for the next NoM release. This conflict was reported for MPP version 1.6.5 but not for earlier versions.
2) Census and Excise Office v 1.3:
The Umbra badge will not show up if the player closes the quest with the MS_Umbra journalindex 70 added by MPP. This has been reported to the C&E developers and will be addressed soon.
Again, I'm not implying any mod is better than any other. I happen to be using all three of these mods and though these conflicts exist, I have no intention of disabling any of them. In fact, I wouldn't care if they were never patched, but it sure makes me feel better to know what caused the issues. Whenever I have a problem that nobody else has reported, I always think my game is buggy and about to die horribly. It is comforting to know this is not the case . . . at least not with respect to these particular issues. Thanks to all modders everywhere for sharing their work.