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?
Best Answer
Easiest way is to note the players perception skill (and other useful info) on a stat reference block and make the roll yourself.
This means you're making a roll for some reason however, which may get the players meta hackles twitching.
An option to avoid this that doesn't even involve rolling a dice (if you don't even want that to be seen) is pre-roll a load of d20's on a scrap of paper; cross each one off as you use it in turn for these "secret rolls".
Or you roll extra d20 random rolls all the time, for no reason at all. This has the added advantage of making the players more paranoid ;) (this is rather than the players making extra pointless rolls) you can speed up this with coloured dice with one colour per player and roll a bunch of them.
Hopefully however players can simply ignore these perception checks without the meta. Related: ( How do I use Passive Perception to have some characters notice parts of the environment? ) Never forget "Never ask your players for a skill roll you don't want them to fail."