In some instances, mag manager will not accept comma-separated values for things like attribute options. This occurs even if you have set the correct delimiter in your import.
Often in this case it will only accept the “|” character. Try using find and replace to swap your delimiter (normally a comma) with the “|” character.
To verify this, and potentially identify a different character your mag manager is accepting, try adding some options to an attribute and exporting a product with that attribute, selecting multiple options for it. Although the export will ask you to specify a delimiter, it may export the data with a different one. Use this one on the import and the problem should resolve.