I tried merging a few of Illy's head/face mods since I'm running out of room.
So I used the TESCS Combine plugins feature.

According to TESAME, the result has half a dozen CELL entries in it that weren't in any of Illy's head mods (they were only BODY entries I believe).

Why does TESCS stick random CELL entries in the result?
Would it have helped if I avoided choosing Morrowind.esm as an active mod here?

Also, if the LGNPC merge I made had similar problems, how in the world would I ever find them?

Thanks!

The CS almost always add some Wilderness cells to every esp. (not sure why, it just happens)
They are safe to remove, and it's best to remove them, so that the esp is clean of them. They are easy to see in EE or TESAME.

You cannot set an esm as the "Active File" and there is no way to load anything in the CS without the Morrowind.esm

Yeah, the CS likes to randomly add things to mods when you save. I recommend using Tes3cmd. I have used it on every mod I have and 95% have these kind of unwanted addtions.

Put Tes3cmd in your data files folder.
Go to the Morrowind directory
While holding shift right click on the data files and select "open command window here"
In the box that pops up, type "Tes3cmd clean " , that's it.

Alternatively you can type "Tes3cmd fixit" and it'll fix all the mods at once. I runs extra things when you do this, such as synchronizing headers and creating a multipatch that will restore changed cell names if one mod changes a cell then another changes it back to the default.

Wow, thanks Pinkertonius.
tes3cmd looks awesome and I think I'll use it all the time from now on.

Yes, it does find problems in 95% of mods.
Also, it even has a --junk-cells option (included automatically in the clean command) for the specific problem I had.

No problem. Glad it worked for you . I love that program (thank you John Moonsugar!). I was stunned at some of the mods, and how "dirty" they were (mostly older ones). One mod had 150+ dirty cells!

I have actually made myself a couple batch files for it, then I made a shortcut on the desktop to it. That way I can "drag and drop" a mod from it's individual folder onto the shortcut and it'll clean it and put the "clean" version right back in where I dragged it from. Using the shortcut, I can "clean" mods not actually in my data files folder. Thought about uploading them but not sure if it's something people would use.