If you havent already tried it, I suggest simply asking them to refund that excess immediately rather than offsetting it against next year's bills. Preferably by email rather than phone, so that there is a record of your asking and of their response, which can be useful if you need to take the matter further.
Regarding the meter though - as it has to be read manually, I presume that it isn't a smart meter? I would ask Thames Water if they can remedy that right away, so that future bills are not based on wild estimates.
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