Thanks for the query.
During embryo transfer
there will be some manipulation at local genital area.
That may be the reason for your pain during urination.
As you are getting the urine normally there may not be any trauma to bladder etc.
And this may not affect the fertilization.
If the symptoms persist you can take symptomatic treatment.
Take plenty of water and analgesic
For more details you can ask me through: http://www.healthcaremagic.com/doctors/dr-sree-gouri-sr/63429