I hate when that happens. Too bad it happens a lot. But I have noticed what kinds of things I don't ever get.
1) something related to unwritten rules those "common understandings" that I never understand.
2) If it involves predicting the end result of something into the future or through multiple steps - um my brain doesn't go that far in a straight line.
3) I tend to be very literal. My brain goes with the first available interpretation. Other people don't seem to have the "option" package in their head, or else they are able to select an option that is more relevant.
4) The situation gets sort of mixed in with my ADD internal distractions and I just assume other people are in the same universe as I am.
Knowing some of the reasons doesn't seem to help me "get it," but I can identify where I went off the beaten path most of the time.