That could be due to you not putting the N.C. (no connection) "X" on the unused pins of the components. A while back they changed the net error checking for every pin not just the used ones before making the PCB, so you can make sure you don't have errors on your PCB and you find them when it's too late. If a pin on a component is unused, put the NC cross on the pin. It's a bit of a hassle, but if you do it from the beginning, it's not so bad. Also, if you're completely sure that you don't have design errors, you can ignore them and continue on working. The image below is from a project of mine\. You can also see that I have 52/136 nets without errors\, but most of them have errors due to not being connected to their corresponding component yet\. I have a pin header for a 16x2 character LCD where some pins are left hanging and some with the "X" on them\. The LCD\_8 and LCD\_9 have net errors\, but LCD\_7 and LCD\_10 don't as they have the X on them and others are connected to some other point\.  I hope this answers your question and helped you in some way!

Thanks for the explanation, I don't have any unused pins on anything, I keep with it unit I see every connection in made.  I do have three connection i would expect, as the pins get a copper trace that a connector is soldered to. As I mentioned, every connection is being identified as a problem. That is what puzzles me.

Which project is this happening to? If you share which one it is, it could help us look at it and see for ourselves.