Nobody has axed yet, but I'll mention it as I'm sure it will come up.
We've had issues in the past with couchmanagers and Yahoo disagreeing as to position eligibility. So someone would draft Jermaine Dye to play OF, but he was only eligible at DH for instance. So you could come down to the last round and have only the spot for one more OF even though you technically had it covered and would rather take a 4th catcher.
In the past we've done 2 things to account for this. One was I would make the roster very very flexible so that most players could play almost anywhere. This also meant you had to do more work to assign which players were actually in which spots. I set the rosters pretty much as defined this year, seems to be working ok so far.
The other solution has been to add an extra round to the draft, basically adding one more bench spot to your roster in the event couchmanagers won't let you take who you want in the last round. I did this, that's the wildcard spot you see on the roster. I will only enter 27 rounds in Yahoo, but couchmanagers thinks we're drafting 28. Let me know if you foresee any problems with this and we'll try to get things adjusted if needed.