When I last saved my game I had 6 secret markers showing on my map. On loading the saved game the markers have now disappeared.
Re-doing the action that got me the markers in the first place fails with an already completed message (I'm trying hard not to spoil this directly for those who haven't done it!).
Additionally my map looks a little weird now. I've got the normal location markers showing in the town, but way down towards the SE of the map screen I've got a bunch of location markers corresponding to upper or lower floors from the town locations (e.g. Cook's House - Cellar). There's no discovered scenery around them, just the markers.