Should I 'admit' a weakness of a paper even if it's 'obvious'?
I wonder if your research is ready for prime time. Not getting consistent results and not knowing why is a fault. Maybe you should continue work for a bit. 

But for the question itself, it is better that any shortcomings come from you rather than from someone else. 

At a minimum, you have an interesting "future research" section to write. Maybe you should find a way to look at the larger data sets or others that will give you better insight into what is really going on.