You took a morning-after pill not on the morning after, but once you noticed that your periods didn't come? That is not the kind of timing that would suggest it worked to prevent a pregnancy, but it certainly could have upset your uterine lining. A woman's periods are often kind of unusual after having had the massive hormone dose involved in a morning-after pill. This should have been clearly stated in the package insert. Don't be surprised by an unusual period after taking it.
If this just happened today, and if you can get hold of a pregnancy test and take it immediately, you *might* be able to detect a trace of hCG with the test. If it is there, (meaning, if the test comes up positive), that would indicate you (at least had been) pregnant, which might let you guess what the clot might have been. But hCG doesn't stay in your system long after a miscarriage (if that was indeed what the blood clot was about, rather than odd bleeding because of the pill itself). The morning-after pill doesn't prevent a pregnancy that has already implanted, so if you took it only after noticing your period for the month was late, if this was a pregnancy loss it would not have been caused by the pill.
It seems like the strongest possibility, however, is that it was some of the bleeding that comes after taking a morning-after pill. It might take a month or two to get regular.
If you don't want to be pregnant, get back onto regular birth control. Morning-after pills are meant to be used maybe once in a couple of years if that often. They are a shock to the system, and not good for you, and are not intended to be used as regular birth control.
It is really common to have irregular bleeding for 2 to 3 months after taking the morning after pill. Emergency contraceptive is a big whopping dose of hormones which is how it works. It most often prevents pregnancy if taken within 3 days of the sexual encounter but then all those hormones are also in your system. They cause your body to react. I would guess this is what is going on with you now. good luck