Please see a demo of this issue at this link.
[all[missing]] works inside advanced search.
But it does not work inside Commander combo search.
This is by design! There were some discussions in past on missing tiddlers. You can find them in closed issues.
If Commander processes them, then any operation will create all of them and this a side effect.
I see. I was trying to add a tag to some selected missing tiddlers, which in effect, would create them, which is what I wanted to do. I then had to manually added tags to those tiddlers. 
You can use https://tiddlytools.com/#TiddlyTools%2FSearch%2FFilters to do this.
To install, just drag-and-drop the above tiddler into your TiddlyWiki.
To tag selected tiddlers, just enter your filter (i.e., “[all[missing]]”), and then press the “tag” button from the upper right “function” icons.
A modal dialog will appear, listing all matching tiddlers, with checkboxes adjacent to each. Press the “none” button (lower left in the modal footer) to deselect all matching tiddlers. Then use the checkboxes to select the tiddlers you want to tag.
Enter the tag value in the “add tags” input field (or press the down arrow next to the input to select tag(s) from a list of all available tags). Then press the “tag” button (lower right in the modal footer) to perform the action. Note that only the selected tiddlers will be touched, avoiding the problem that Commander has.
enjoy,
-e
2 Likes
Thank you @EricShulman. I had no idea about the existence of search filters plugin. It fixed the issue
I see. Unlike “Search Filters”, Commander adds a temporary tag to all the selected tiddler, which is certainly an unwarranted side effect.
Thank you both.