I'm not certain this is a FATE bug, but I too had this issue. When I had ~5000 seals earned total, it said I had just gotten an achievement for getting 10k. I had ~3000 seals on hand, 2000 buying chocobo license. So there really was no way to have earned 10,000 unless it was counting seals I earned for lower level fates before joining the grand company (and therefore, earned no seals).

Either its doubling the amount of seals for purposes of the achievement, or the pre GC FATE are counting as seals even when you recieved none. I haven't really looked into this issue, but I too noticed the discrepancy at the 10k mark.