My theme league has a 10% salary cap ($10M) and I was given 50 prospects.@ $200K per player so my salary cap is already reached before I can make a single transaction. When I select a player I get a warning msg that I am violating the cap. It appears that other teams In the league have AAA players on their MLB rosters. What can I do?

Waive some of your AAA guys?

If you don't have any $200K players on your major league roster, you really can't do anything. 

The minor league salary cap is a nuisance that really serves no purpose.  It was put in place to discourage the fatigue strategy, but it doesn't deter the strategy at all - a smart owner can easily make the fatigue strategy work.  No theme league should ever have this turned on unless there is a really compelling reason to do so.  I'd petition the commish to submit a change request to admin.