Playing witht the Creus we had a little dispute about how the flagship can move if located in the home system. Since the home system has a D wormhole and the player can chose to treat the destination system as containing a D wormhole, it would be possible for the Creus to chose any enemies  home system as destination and, therefore, be incredibly strong.

How did you guys handle this situation?

I myself am a big Creuss and player I would love for that to be possible but sadly that is not the case. I don't have the link for it as the wiki was hacked into oblivion, but it has been errata'd that at no point can Hil Colish use its own wormhole. You treat the destination system as having the wormhole for the movement purposes of other ships who are moving in to join the fleet.

Correct.  It's as if the wormhole was located ON the flagship; it can't turn inside out and go through the one it's carrying.

There is also the wording on the flagship card to take into account.

If i recall correctly it says: "When moving, treat the destination system as if it had the wormhole." The wormhole (as in only one wormhole) being the important part.