Yes - this happens quite often - as Champ says, usually when the flag is left in.
The bounce you get off the flagstick is unrealistic. You can hit the flagstick on the full and see the ball bounce off and roll 40 yds. This added speed off the flagstick seems to be enough to "bounce" the ball off the bottom of the hole and out. It also seems that the sides of the hole are not "solid objects" as the ball bounces out, otherwise it would only be able to get out straight up. I guess not a lot of programming has gone into how realistic the bounce out of the hole is! (hardly surprising lol).
Bottom line (bottom of the hole line) is that removing the flag prior to making your shot makes a lot of these problems go away.
Note: Removing the flag AFTER playing the shot does not work. Anything you do after playing the shot is only for your visual convenience (like putting the flag back again so you can see where the hole is - the game still considers the flag is OUT).