Electronic – Altium Designer 16.1 Can’t find Pin in Place Menu

This has nothing to do with missing PINs in components. This has to do with that the PINs in the schematic differs from the PINs in the layout. My guess is that you have added components to the schematic and when you validate the schematic against the layout (Validate Changes) Altium can't find the new PINs in the layout. A strange way of the program to say that you have added new pins to the schematic that are not in the layout. This happens often for me as well in Altium.

If you press Execute Changes, I'm pretty sure that Altium will add the new PINs to the layout without giving you any trouble. I'm not sure but if you then press Validate Changes you will get nice green circles all the way.

You probably have edited the the schematic symbol in Sch library after placing its footprint on the layout design.

In situations like this, you need to update your schematic design from library (Tools/Update From Libraries...), then update your PCB with the updated schematic. If problem still there, remove the footprint from PCB file and update the PCB file with schematic again.

Also make sure the symbol in schematic sheet has the same footprint model name as it has in Schematic and PCB libraries.