its usually either One way tickets or tickets bought at the last moment.
And may be some common names (but if that was the case you would have
been flagged before)

fortunately I've only been flagged once. that was for
One way ticket, 2 hours before the flight and my assistant booked
it without using my FF#.

if I buy it using my online account and FF# (with elite status on it)
i've never been flagged .. even for the last minute one ways.

(i've done this on delta, CO, NW, WN, KL)

mostly likely you were flagged in the computer so the
Agent marked it.

i've flown on hand written boarding passes about 4-5 times
last year.. and never had any issue.