The stone of ill luck cursed magic item from Tales from the Yawning Portal appears as a stone of good luck and says:
it confers that item's property while on your person.
The bonus from the stone of good luck is +1 to saving throws and ability checks. Then under the curse section it says:
while it is on your person, you take a -2 penalty to ability checks and saving throws.
Until the curse is discovered, this is done by the DM in secret.
I see two options for how these bonuses could be added.
The stone of ill Luck adds a +1 to applicable rolls, and subtracts 2 as well, for a total change of -1 to applicable rolls. The DM would need to subtract 2 from applicable rolls in secret since the player would be assumed to add the original +1 themselves.
The stone of ill luck only appears to be a stone of good luck, and does not actually add the original +1, only subtracting 2 from applicable rolls for a total change of -2 to applicable rolls. The DM would then need to subtract 3 in secret, 2 for the curse and 1 for the incorrectly added bonus.
Option 1 is definitely easier to run and is nicer to the players, but I can also see an argument that the stone appears to add the +1 while not actually adding anything.