I'm sure this happens more frequently than one would assume. A "secret" clearance is pretty much a credit check and a criminal background check, and costs the government probably on the order (I would guess) of ~$1,000. A TS background check costs upwards of $20,000. 

That said, the TS check kind of "includes" a secret check. I'm sure there are tons of folks out there in low level civil servant jobs that require a Secret clearance who are applying for positions that require a TS clearance. Surely, a few will be denied. 

I think if they're denied for reasons that may also deny them a Secret clearance (i.e., the TS background check reveals concealed bankruptcy, criminal convictions, etc), the Secret clearance may also be stripped. Otherwise (grossly unfavorable comments from a litany of friends, supervisors, etc), the Secret clearance would probably remain intact.

As you say, however, it's probably circumstantial. If the TS background checkers discover something very troublesome, they'll probably inform a supervisor. If it's a judgment call of some kind, and no real red flags, the Secret clearance is probably good to go.