(a follicle is technically a type of cyst). Ovulating cancels the transfer because it produces progesterone too early, making lining out of phase.
They don't like to start if there is a big follicle that might ovulate through the estrogen. Some calm down and shrink as soon as you start external estrogen, especially if they are small, since you stop pumping out FSH once the brain senses enough estrogen.
I did a mock cycle with a fairly large cyst/follicle that was producing estrogen, it continued to grow but then stalled and never ovulated, built a good lining that way, clinic was very happy. But there are also plenty of stories where the patient ovulates and that cancels the cycle.