Here is what I think realistically happened.
1. REM3DS was posted to gamefly website so people could put it on their Q.
2. At that time they knew it would be 39.99 retail
3. When the game came out they placed the keep it price up thinking they were gonna rent the game
4. Saw the save data feature and as a business decision decided to abort renting the game as it would be too unappealing.
5. Didn't cancel keep it price at time because like other retailers they were on the fence about what to do and waited for capcom to give final word on a possible patch to fix issue.
6. Patch isn't coming, gamefly isn't renting, simply forgot to erase keep it price to "not available for purchase"
Simple story that makes sense :).