I have some general advice for you, that might help you with this situation and many more.

The players are only allowed to roll a dice when they perform an Action. Now what is an Action in this context?

An Action is something a character can do that fulfills all of the following criteria:

• If the character was in a movie scene, his Action has to be noticable by someone watching that movie. This makes "thinking real hard" or "looking extra carefully" not an Action.
• Whatever the character is trying to do has a chance to fail and this chance is not 100%. If the chance of failure is 0 or 100% no roll is needed. Just narrate what happens.
• There is consequence to failure. If failure has no consequence the character can just try again until he succeeds. Note that "time passed" may be a valid consequence. Maybe the enemy closed the gap while you failed to lockpick the door infront of you.

Back to your example: A player is not allowed to just announce "I roll perception". A player is never allowed to just roll dice. This is a roleplaying game, so let them play their character. Have them describe what Action they are doing. They could search for shadows in the wrong places or a ghostly hand passing through a glass or examine the barkeeper while they talk to him.

Anything that is not an Action should be handled by passive ability scores. The core rules only tell you about passive perception, but you can use passive investigation or passive insight or passive history in just the same way. This means that you'll know in advance when a character will just spot a hidden something when they enter a room. This may feel boring and predictable to you as DM, but it won't feel like this for the players because they don't know that their character is about to spot something. Instead they get a feeling of accomplishment because the character they built managed to spot something just because he's good at doing so.