It seems to me that this is a simple error, given you'd normally get to City Thameslink from the south. They've simply forgotten to update things to take into account the fact you could now come there from the north.
If you pay for HS1 then it's pretty obvious that you could come from the north OR south, but more often than not from the north (given you've paid the extra), so the ticket should allow for this.
If you're stopped, it's surely not your problem that the ticket is deemed invalid. How else can you get from St Pancras to City Thameslink?
Clearly SET needs to update their systems, but you should not be given a PF and if you were then it should be a 100% open and shut case when it comes to the appeal (as in, you'd win).