Where does the third bearing go in my Dyno moto 7 cruiser headset?
Here's a dyno7 showing where bearings are.

A headset has exactly two bearings, because they preload against each other.  There is no place for a third bearing.
Possibilities

Somehow, someone used two bearing rings and somehow interleaved them.  I can't see this fitting and rolling at all.
there's some form of dust cap that has popped off and looks like a bearing, but the bike should would have identified this straight away
Did you take something else apart - like a wheel or the BB or even a pedal?  Theres a chance a bearing might have got mixed in, or even just picked up from another bike by mistake.
Assembly error - when the bike was put together, someone managed to loose a bearing and retainer down the head tube somehow, and couldn't be bothered fishing it out.
Spare - a previous owner intentionally stored a new bearing in there, under the headset cup.

If the steering is working fine with the two bearings installed by the bike shop, then roll with it. (literally!)

Later thought - does yours have the original cantilever brakes on the front wheel?  Could be someone's done something weird with the brake hanger, which was mounted above the head tube.
There shouldn't be a third bearing there - the hanger is clamped around the steerer just above the top bearing.   Better photo: