The 10,000m records were thrown out after the course in Glasgow was 150m short.
The area wasn't laid out in line with the plans.
Paul Foster of the Great Run Company apologized to Eilish and explained the situation.
The Great Scottish Run fell short again after the half-marathon course was found to be 150m shy in distance.
In this year's men's half marathon, the record was set by the Scotsman, who won in 1:03:35, ahead of the Craig brothers.
The error had a small effect on the half marathon, but it was within tolerance and the course was valid.
After her first major title in the Commonwealth Games 10,000m, a silver in the 5000m and two medals in the European Championships, the Dundonian's stand-out year was capped by the records.
After withdrawing from the London Marathon, she ran in the Great Scottish Run, shaving one second off her previous best in the race in Glasgow.
"We are going to review our internal processes to make sure we don't make this mistake again," said Foster.
We are very sorry and there are no excuses. We are aware that we let our customers down.
Several extra check steps have been put in place to make sure the situation won't happen again.
The first Great Scottish Run in three years was held this year and was attended by 20,000 runners, who did 10,000m or half Marathons.
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