Me temo que me has malentendido.

why is this not hayas malentendido?

My dictionary states that the pronominal verb (i.e. temerse) is used for politeness:

(en fórmulas de cortesía) to be afraid
▸ me temo que no puedo hacer nada más
I’m afraid there’s nothing more I can do

whereas the transitive form is used to express actual fear:

temer que + subj:
▸ teme que le echen la culpa a él
he’s afraid that they’ll blame him for it

Politeness is probably the reason why the subjunctive is not used in the first case, that is, you’re not actually expressing an emotion, in contrast with the second example.