So, their entry and exit stamps have overlapping dates? That sounds odd, it must be just the validity dates of the waivers...Did they come, leave, and return together?
And anything that seems off may kick off some alarms at the immigration booth. This year I was detained briefly and questioned (albeit in a friendly way) about my activities last year, because I stayed almost the whole 90 days, went to Korea for two weeks, then came back for a month before flying home.
I would try to nail down an answer to be sure that the clock resets on January 1st, so that their time in Japan within a year of this coming visit doesn't count against them. I believe that's how it works (keeps it simpler) but I'm not an authority.
Just make sure they know that because of their visits last year, they may have some extra questioning to deal with, but the purpose of this is to make sure they aren't working illegally. It would be helpful if they knew the exact dates they came and left last year, since it's likely they came BACK on March 4th, which is why the second waiver starts from that date.