"I am sorry if I am bothering you."
Translation:Mi bedaŭras, se mi ĝenas vin.
Would "Pardonon, se mi maltrankviligas vin" mean the same or something a bit different?
It would be more like "Excuse me if I am worrying you" or perhaps "...if I am making you nervous".
Not the same as "bother" which could mean things such as "being too loud" or "being in the way".