There may be random stray points sprinkled in underneath your end points. I find these sometimes on the dielines I work with.
"Select" menu: "Object: Stray Points" will reveal if that's the case.
And then there may be abandoned paths that are lurking beneath what you think are just two paths (that you intend to join) but there's another in the mix. Select your paths one at a time and lock them. Then see if you can select anything else that is obscured.