We can say both misshapen and misshaped. Where does the misshapen form come from? What other words use this form?
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Misshapen comes from shapen, originally the past participle of to shape. This ‘strong’ -en ending for past participles survives in a few other verbs as well: e.g., eaten, gotten (also begotten, ill-gotten), taken, fallen… (Wikipedia gives a longer list, and some historical explanation.) However, in these cases, the other forms of the verb have also remained irregular.
I would guess that in the case of (mis)shapen, it was semantic detachment from other forms of the verb — (mis)shapen getting used as an independent adjective, not considered just as a form of the verb to shape — that allowed it to keep this form while the rest of to shape regularised around it? According to the OED, it was during the 14th–16th centuries that most forms of to shape became regular; since the 16th century it has been completely regular, with normal past participle shaped; but shapen as an adjective was in use into the late 19th century, and misshapen survives today.
(Compare also Kosmonaut’s excellent answer to “Why are clothes hung and men hanged?”)
I believe the -en ending is indicative of the past participle form of some verbs. This form is frequently used as an adjective, e.g. broken glass, written word, fallen soldier.
For misshapen in particular, dictionary.com does identify it as a past participle form of misshape.
According to EtymologyOnline,