Here, "take account of" means "include, among the factors contributing to something."
"I think Saturday would be a great day for a picnic in City Park."
"You're not taking account of the mosquitoes. They're awful there at this time of year."
An example that is closer to yours:
"I check my weight weekly on my bathroom scale."
"Yes, but the scale doesn't take account of what percentage of your weight is body fat."