This applies to all d20 systems, but with an example from the from the Pathfinder PRD (emphasis mine):
Stonecunning: Dwarves receive a +2 bonus on Perception checks to potentially notice unusual stonework, such as traps and hidden doors located in stone walls or floors. They receive a check to notice such features whenever they pass within 10 feet of them, whether or not they are actively looking.
In this case, does the GM roll the check in secret or ask the player roll the check?
If the GM asks the player to roll for the check, what stops situations like:
GM: (interrupting) "Gimli, Roll a perception check."
Dwarf player: "Oh, it's a natural one, I guess I don't see anything."
Human player: "Okay, I'll roll a perception check for anything unusual in this room. Nice! 19. How about 19, does 19 work for you?"
GM: "Gimli, everything looks kosher to you. Aragon, you notice a rock coloured tarp on the ground here, covering what looks like a pit trap."
In this case, by telling the dwarf to roll his "free" perception check, he's telegraphed to the players that there is something to notice.
How can this be fixed, without bluffing checks for nothing in particular to throw off the signal to noise ratio of similar checks?