I don't know a literal translation.
In a casual way (slightly serious look on face):-
1) Sorry for all the trouble, or 2) Sorry for bothering you.
"不好意思, 辛苦你了" may be a regular thing in China but I'd avoid making a habit of apologising in this way.
"Thanks for all the hard work" or "Thanks for your effort" (with a smile) would probably come across better.