What they are doing now is called washing the money, and then reprinting a new copy over the old paper. it will test alright with the counterfeit pen. Also will show the line down the side as normal. What you can usually spot is the face that's embedded in the bill on the RH side as a hologram, they can`t wash that. I caught a $100.00 bill before depositing to the bank from my business not long ago that looked ok, until I held it up to the light and saw Lincolns hologram face on the right, Ben Franklin should be there.
Noob cashier.
That's the best way to quick check a for a counterfeit.
If it was more than one he new about it. Probably rationalized he could scam you since it was counterfeit goods and you probably would`nt report it.