Are you sure it is a cyst? Because RCT is not the treatment protocol for a cyst. There are only two ways to manage a cyst: enucleation, or marsupialization. Maybe it is an abcess. That would explain why pain is felt. Because pus inhibits the anesthesia from working, and abcesses are files with pus.
So... Assuming that it is an abcess, do not worry. During the next appointment ask your dentist to use more anesthesia. Since the RCT is going on, it will get better within a week.
Next Steps
Consult with your dentist about the problem.
Health Tips
See... you need to understand that any medical procedures take time. The RCT is not over yet, so wait for a few days. And communicate with your dentist about the problem. Only then he will be able to fix it.