Problem with expl3.sty

[Karl Berry]

    We've seen this repeatedly,

I don't doubt your observation.  Please provide a recipe to reproduce. 

The only way I see tlmgr invoking fmtutil-user is if --usermode is
explicitly specified, which I doubt these expert users are doing. (I
also presume they are not explicitly invoking fmtutil-user.)
Maybe I'm missing something.

    with some users who definitely know what they are doing ...

Or maybe that's the problem :). -k