Bottom bracket is ticking
Bottom bracket noise is a frequent problem, and often hard to diagnose.

First and foremost, check the tightness of the crank bolts.  (Your LBS should have done this when they checked out the bike.)  A loose crank bolt can be the cause of BB noise, and failure to tend to the problem immediately (if not sooner) can result in irreparable damage to the crank arm.

After that there are a number of possible causes.  On a non-derailleur bike the chain may simply be too tight.  On a derailleur bike the chain may have a frozen link.  There may be a bent chainring tooth, or a deformed chain link.

Rarely, the problem can be due to bearing problems within the BB, but much more often with BB cartridges the cups have worked slightly loose and the cartridge is sliding back and forth in the housing (harmless and easily fixed).

On bikes with loose bearings (vs a cartridge) in the bottom bracket a loose cup can allow the crank to actually tilt slightly, such that the chain hangs up on the sprocket.  (This is easily diagnosed by simply grabbing the crank and shaking it -- there should be no bearing play detected.)

And pedal bearings seem (to me) to go out with aggravating frequency.

Then, of course, there's the "trick" knee or ankle that clicks sometimes.