The problem comes when PTFE/teflon is subjected to very high temperatures, as seen in gunbores during firing.
The teflon outgasses hydrofluoric acid as a combustion breakdown product. The acid eats the chrome and/or rifling out of the bore over time, causes stress fractures, pitting etc. Exposure to acid is bad for metal. Hardchrome as found in AR15/m16 barrels is particularly susceptible to this.
From the Eezox
For example, Teflon is fine for frying pans, gears and other metal surfaces, but it is not a lubricant. Teflon, in fact, builds up residue when blended with flammable petroleum lube distillates. This residue build-up is left on firearm mechanisms, firing pins and in bores/barrels, etc.