I assume you are talking about the HPV vaccine, and not the virus itself. She said it felt like a stone in her arm? It sounds to me like she is having some sort of allergic reaction to something in the vaccine OR the vaccine was not stored properly and has caused this reaction. I suggest you call the doctor.
I've had a lump under a vaccine site previously. The lump usually goes away in a few days. Once, the vaccine wasn't stored correctly and I had a lump for a few weeks.
To be safe, call the doctor.