If I assume that the parts on the boards are all correct, then there are errors in both the schematics and the parts list. Some are just incorrect in the parts list, some are just incorrect on the schematics, and some on both.
However, on the trigger board (where I am working now), C134, C330, and C333 have 0.01uf caps installed. My scope is an Option 5, and on the schematic it has 0.1uf marked for those, and the parts list also has 0.1uf marked. They are all decoupling caps. My guess is that whoever did the last change-out of all of these caps (probably sometime back in the 80's) they used a manual that was not for the Option 5 model, and installed 0.01uf instead of 0.1uf. Since both the parts list and manual have 0.1uf specified, I am going to switch them to that value. I think it's highly unlikely that both the parts list and schematics are both going to be wrong.
For any such future discrepancies like this, if both the list and schematic have the same value marked and it is different from the installed part, I am going to change the value. If I cannot decide, I will refer to other revisions of the manual. As far as I know, the schematics I am using are the most recent. They are a "MAR 1981 Revision" set.