Nested duplicated MLB Players list

For Item 2, you need an additional piece of info to make each player unique e.g. birthdate, middle name, height or something.  Hopefully you can add it to your data early on in the process and without doing it manually but if that's the way it has to be done, then that's what you have to do.

Item 1 isn't really a problem - it just depends on what you are using the data for.  It works as a Fact table, if you want to keep track of the different positions players have.  If you want to use it as a dimension table, then use a primary position field or get rid of the positions and remove duplicates.