The usual morning after pill is a large dose of progesterone, designed to prevent ovulation for at least five days. As it happens, you probably weren't going to ovulate in that time anyway, but in any case it's extremely common for it to disrupt your regular cycle.
You can treat it as a sign that you're not pregnant, and confirm that with a test in about a week (Poundland etc tests are much cheaper than the big names and just as reliable).
Your cycle will settle down again, probably quickly. If you're worried, you can see your GP.