The most common is an infection, either bacterial or fungal, in the uterus. Usually, once the infection is treated, fertility is restored. Some mares are "windsuckers" - they tend to pull air into their uterus, resulting in a higher risk of infection.
In maiden mares, sometimes the cervix is so tight that sperm is retained in the uterus - which can also cause infection.
Chronic infertility can be caused by, well, all the things which cause infertility in human women. Uterine cysts are common in older mares. Blocked or deformed oviducts, tumors, and missing uterine horns have all been observed in horses.
I once knew a mare who never went into heat in her entire life. She likely had a disorder of sexual development - i.e., she was intersex. Turner syndrome (Missing chromosome causing stunted growth and deformities), sex-reversal syndrome (SRY gene missing from the Y chromosome), AIS (in which a male fetus doesn't respond to male hormones and develops apparently female) and XY/XX chimerism (which may or may not affect fertility) have all been observed in horses. With the mare I'm thinking of, I suspect sex-reversal syndrome.
A final cause of breeding failure is the mare rejecting the stallion chosen for her. These days, artificial insemination is often used, but in Thoroughbreds, where it is not allowed, it may even be necessary to change breeding plans.
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