They aren't 'coming up with the timings' The timings are preset by your meter which has two rates. The heating and hot water will only come on during the off-peak period and your meter will record off peak usage during that period. Again, on-peak, the meter will record usage during that period on a separate register.

You are billed by the meter readings from the two registers on the meter.
It's still not clear from the OP whether they have a 'dumb' Economy7 meter or a 'smart' meter configured for 2 rates.
If the latter, then there is plenty of opportunity for it to be misconfigured so the switched load timings don't match the tariff timings.