Just one cyst isnt a problem, don't worry. Lots of mares have them and it rarely affects breeding, unless they have hundreds of course!!! Cysts can come and go, your vet may scan her in weeks to come and it may have vanished. They seem to grow and recede during the mares cycle. I would say that you were just unlucky your girl didnt get in foal. Take it from me there are a lot of people whos mares arent conceiving this year, I think its the darn awful weather!!
Don't worry! My mare who is 21, has loads of cysts and she is pregnant. What can happen is that the fertilised egg can come to rest against a cyst and cannot implant properly. Next time may be better.