I would go with "I'm sorry that you've misunderstood me"... or "I'm sorry you've taken it the wrong way"...
By me saying sorry I've accepted that what I have said or done may not have been communicated clearly or I may have said it with a presumption of a particular point of reference... leaving room for any possible point of view that is different from mine.
I could also just be sorry that they are limited in thier scope too
