If your earnings rules / pay rates are not applying correctly, check these steps:
Check your pay rates and their applying rules.
Check which rule is applying to the timesheet and shift in question.
Check the user has the correct tags for the rule.
Check any other conditions for the pay rate and check they apply to the certain timesheet / shift.
If the rule applies to bank holidays, check that bank holiday dates are setup correctly on your account in settings > general.
If a different rule is applying than what you expect, check there are no rules with overlapping conditions.