First of all, you do not have to manually add games. Use the fix missing option or the rebuilder (which acts as an adder).
The Scanner Results Tree window shows detailed information about the issues which were found. Expanding a set branch shows you the filename, the error, checksums, sizes etc.
"why would they show up in a socond scan if the same games didn’t show up the first time around"
If you've added a wrong set manually or didn't use the right storing method, cmpro will of course show a message, e.g. about unneeded files.
"When I scan i get a list of missing roms, for example DigDug is reported missing. When I check the folder with the romset there is several versions of DigDug"
Beware: the 1G1R mode is a special thing. It uses one more or less generic setname and selects 1 set (parent or one of its clones) to be the chosen one for this setname. All others will be obsolete then. The files which are put in the set are taken from a language/reagion logic.
So if you have a DigDug set there it does not necessarily contain the files which the 1g1r algorithm wants to be in there. So you might have a set DigDug.zip with a let's say japanese rom version file in the archive while the 1g1r algorithm picked the english one for it. Such things can be of course resolved by e.g. rebuilding the sets.
For more help, I'd need to see the exact message and more information about what is stored in your archives on your system.
Starting with the 1G1R mode is a big step in case you're new to cmpro. First things would be to understand parent/clone relations, the merging concept, the official storing mehtods...and then the 1g1r mode
Regarding storing methods:
For decompressed sets: rompath\setname\file 1...file n
For compressed sets: rompath\setname.zip (.rar/.7z) where file 1 .. file n of the set is in the archive