There may be some occurrences where totals in Cost History do not match Flex Reports or AWS Cost Explorer despite no obvious issues. This may be due to some charges falling into different months.
The Cost History report is based on the "UsageStartDate" presented in the Cost and Usage Report (CUR) from AWS. FlexReports, however, are based on the "BillingPeriodStartDate". Since these two reports are referencing different time columns, there can be situations were line items may fall in one month in one report and a different month in another if charges/usage are on the last day/first day of the month.
Be sure the check totals of surrounding months to reconcile the discrepancy is due to costs appearing in different months.