Sounds to me as tho the AF was in the pool for some time, or he either A: made to pass on it and lotted, never saw the lot because of chat log spam, and never corrected, or B: he made to pass, lotted by mistake, and the timer ran out and dropped to him before he could pass. In either case, bummer to the person who lost it, and bummer to him because now hes in the lime light and has an inventory slot taken up by a piece he'll never use and has to drop.
In my experience, ninja lotters won't tell you that it was mistake unless they know you'll believe them. Be they a long time friend or long time LS member, ninja lotters are usually newer people to the shell who show up for a few runs, accumulate some points, ninja lot the piece they want, then duece out anyway.
Since this person is a sack holder, you (or your leader, if your not) obviously has trust in this said individual, and said individual has earned that trust. This may be a blow to that trust, but thats the repercussions of mistakes. If he is a legit ninja lotter, he's built up enough trust to get in tight with the LS leader (you or otherwise), and I may not agree with it, but congrats to him for successfully manipulating your (or LS leader's) fragile wittle heart.
Proper course of action from my perspective, he continues to lot currency, as Wooooodum put it, he is doing you a service, but cannot lot AF for the next run, and wait it out. If he ninja lots again (and especially if its the same job's AF), you can safely assume hes a career thief and rightfully verbally bash his name in these forums as other people have done in the past. If he doesn't, then your no worse for wear, and can continue as previously done.
I do agree with Wooooodum on the account that I don't believe that you believe he is guilty of purposefully ninja lotting, because you failed to supply name, AF lotted, shell, or server, which is usually what people do to make a warning of a ninja lotter known.