What does the SRD tell us?
Trap Floors
Some floors are designed to become suddenly dangerous. With the application of just the right amount of weight, or the pull of a lever somewhere nearby, spikes protrude from the floor, gouts of steam or flame shoot up from hidden holes, or the entire floor tilts. These strange floors are sometimes found in an arena, designed to make combats more exciting and deadly. Construct these floors as you would any other trap.
This is an example of a lever doing something bad. Heck, this is an example of a whole lot of bad things levers can do.
A special door (see below for examples) might have a lock with no key, instead requiring that the right combination of nearby levers must be manipulated or the right symbols must be pressed on a keypad in the correct sequence to open the door.
Hmmm. Here a lever does something good. This may, perhaps, supply a reason why the PCs in the OP might think that the lever and secret door are a combination?
Shifting Stone or Wall
These features can cut off access to a passage or room, trapping adventurers in a dead end or preventing escape out of the dungeon. Shifting walls can force explorers to go down a dangerous path or prevent them from entering a special area. Not all shifting walls need be traps. For example, stones controlled by pressure plates, counterweights, or a secret lever can shift out of a wall to become a staircase leading to a hidden upper room or secret ledge.
Shifting stones and walls are generally constructed as traps with triggers and Search and Disable Device DCs. However they don’t have Challenge Ratings because they’re inconveniences, not deadly in and of themselves.
Hmmm...another bad thing that levers can do.
Apparatus of the Crab
This item appears to be a large, sealed iron barrel, but it has a secret catch (Search DC 20 to locate) that opens a hatch in one end. Anyone who crawls inside finds ten (unlabeled) levers: The device has the following characteristics: hp 200; hardness 15; Spd 20 ft., swim 20 ft.; AC 20 (-1 size, +11 natural); Atk +12 melee (2d8, 2 pincers).
OK, this is a good thing that levers can do....but in this case they are part of something very specific.
Crossbow, Light
You draw a light crossbow back by pulling a lever. Loading a light crossbow is a move action that provokes attacks of opportunity.
Crossbow, Repeating
The repeating crossbow (whether heavy or light) holds 5 crossbow bolts. As long as it holds bolts, you can reload it by pulling the reloading lever (a free action). Loading a new case of 5 bolts is a full-round action that provokes attacks of opportunity.
You can fire a repeating crossbow with one hand or fire a repeating crossbow in each hand in the same manner as you would a normal crossbow of the same size. However, you must fire the weapon with two hands in order to use the reloading lever, and you must use two hands to load a new case of bolts.
Again, pretty item specific.
"Lever" also shows up in the spell, telekinesis, which can specifically be used to operate a lever.
So, if we exclude ourselves to what is in the SRD, and if we know the lever is not part of a crossbow or an apparatus of the crab:
Good possibilities: Open a door, shift a wall to open a door.
Bad possibilities: Make spikes protrude from the floor, make gouts of steam or flame shoot up from hidden holes, make the entire floor tilt, trap you in a dead end, prevent escape out of the dungeon, force you to go down a dangerous path, or prevent you from entering a special area.
Do still you disagree that, within the concept of dungeons promulgated by the Core Rules, pulling a lever (unless it is part of your equipment) in a dungeon-like setting has a disproprtionate chance to make something bad happen?