I have a pretty good guess for why you fail to reproduce it. :-)
When entering the filter strings manually, it is impossible to enter a raw TAB character (since this will only cause the GUI focus to change to the next control), BUT when doing it from a macro it can be done, without the TAB character being escaped!
More specifically, I do like this (which is part of my normal workflow):
I first select some text containing (among other things) a TAB character, and then execute a macro constituted by the following line:
document.Filter(document.selection.Text, 0, eeFindKeepPrevious | eeFindNegative);
You will then clearly see an unescaped TAB character in the filter list inside the EmEditor GUI, and it will also tag along to the export file in case of a filter export, in turn messing up the structure of the TSV file produced by such an export, and consequently making these lines of the export file impossible to re-import.
So, the solution would then seemingly be to make sure that special characters like TAB are automatically escaped also when using macros to add filter levels containing them.