How long were you in the graveyard? Saving was disabled while underground there due to a problem with those cut scenes; once you kill Jake you can save. If the game detects that a cut scene has not completed after more than 10 minutes, it pops up message saying that there may be a problem. If you have not run into any problems, the message was probably just due to Jake's cut scene.
If you want to see the message, check out
Potential Problem Warning for a link to a screen shot.
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