I use only manual saves. With about every second or third save, when I load the save I get a CTD either as soon as the loading finishes or within 2-5 seconds after the scene appears. The other saves load normally. Both indoor and outdoor saves are affected. I do get occasional CTD's during the game with no apparent trigger, though they are not nearly as frequent as the crashes after loading. I use MGE and launch the game from MWE. Affected saves crash the same way even when loaded from the Morrowind launcher, after the usual error messages about MWE not being loaded. Wrye Mash shows no problems with the save files, and MLOX suggests no changes in load order. I have no similar problems with Oblivion or Fallout 3.
Load List:

What does your Warning.txt say after the crash? There might be a clue there.
There have also been reports of MWE causing these type of problems with Save files, but I never use MWE so I'm not familiar with them.

The Warning.txt has only the following:
Unable to find script 'ASH_Zombie_S' on object 'ASH_Dead'.

That's the same error message I always get during loading, apparently related to an error in the Alchemy Storage Helper mod. This same error appeared in my old Morrowind installation and never caused a problem, so I think it isn't related to my current crashes.

Do you have any links to the MWE reports?

The crashing appears to have been solved by deactivating the Oblivion-Style Spellcasting mod. I really liked the function that mod supplied but it wasn't worth the crashes.