Yeah this has come up a few times. The problem is that flex return is based on SP earned, and if you build a player "Experienced", he earns SP as if he played all season. Well, no, that's the reason. The *problem* is that "experienced" is selected by default, so if you're just messing around with player creation, you are likely to hand some flex over because you forgot to deselect the box.
Some suggestions to fix that here:
http://glb2.warriorgeneral.com/game/forum/thread/5138478