Hey hun. Sorry you had to go through the pain that is the unholy cysts of medicated doom. (Sorry for the exaggeration, I just hate cysts with a fiery passion...) Hopefully you won't have to deal with that again this cycle.
Optimal follicle size on Femara is 25mm. Doctors will generally trigger at 20+mm, but best results occur when doctor let the follicle get to 25. Ovaries can develop cysts in any medicated cycle, it's just a risk that comes along with the meds and has nothing to do with follicle size at trigger.
Technically, ovaries develop a cyst every cycle you ovulater. After the egg is released, the follicle turns into what's called the Corpus Luteum. Technically, the corpus luteum is a cyst-type structure. The CL produces progesterone, which finishes development of the uterine lining and keeps AF away. If you get pregnant, the CL keeps functioning, if you don't it dies off, progesterone drops, and AF arrives.
In medicated cycles, you generally get triggered with hCG. With your hormones already out of whack, the CL can get really agitated by the hCG and start growing in ways it is not supposed to. This can also occur in women who are TTC naturally and become pregnant. The hCG from the pregnancy rises and it messes with the CL. (This is way more likely in medicated cycles because the body is already so hormonally messed up.)
When this happens, the CL becomes a mean, awful, raging cyst. At best, it just goes away on it's own. (This is most likely, but if you're trying to move ahead with treatment, the doctors will offer puncture the cysts to speed thing along.) At worst, you end up with severe OHSS. Neither is comfortable at all.
If you are pregnant with cysts and they get really bad, doctors can remove them and supplement you with hormone treatments. However, if you don't have severe OHSS, they will often leave the cyst as is it since it is still producing the progesterone that the pregnancy needs to survive the first couple months. Usually, the cysts resolve themselves by 12 weeks.