My pinky toes used to hug their neighboring toes and it was actually quite painful as I transitioned into VFFs and forced them to go back where they belong. Give it time, they will adjust and you will be able to wear VFFs pain free.
Yup mine too. It took a couple of weeks until they started to complain less and less. And a few months until it stopped feeling weird. But now my little toes don't give any trouble at all and they are much more separate from their buddies even when I am fully barefoot.