Often items shipped with free shipping will be sent on the slower option available to save the company shipping dollars. This is often the case with ON/Gap/BR/Athleta. Sometimes it will even indicate this fact when choosing a checkout option.
Other times it can actually be a company issue with the warehouse, although that would be more rare. Something going on behind the scenes like inventory, switching warehouses used, etc.
And of course, there can be shipping mistakes too.