Muscle Pain when Botox For My Migraines Wears Off

No Botox injections does not cause nerve damage.  It paralyzes muscle to reduce compression of the nerves that can trigger migraines. 

If the nerve had been injured you would be expected to have had pain since the treatment despite not having migraines.  The Botox is not an anesthetic so you would know if you had the nerve pain from Migraine treatment with Botox injections. See a neurologist. If you're still not sure or the neurologist is unsure, possibly nerve conduction tests could be done to determine if the nerve is injured.

If Botox  caused nerve damage you would have had symptoms when the injection was done, not when the Botox starts to wear off. First, I would consult with the neurologist or physician that treats your migraines; he may want to change your prescription routine.