These are fixable by you. Just make yourself commissioner, then when you go to the player profile you will see there is a tab for Editor. On the editor page for each player there is the ability to fix contract problems. In the case of Jack Cust, you can do that by simply making his contract for one year. You can do the same for Duchsherer.
If there are more sophisticated things you want to do (like option years), the manual can help with this.
My guess is that these things probably won't be dealt with in a future patch. Could be wrong, of course.
