Hi Stephen,
You will have been charged a zone 1-2 cap and two extension fares between Slough and zone 3. Unfortunately neither TfL nor the train companies will publish what these extension fares are, so it’s all a bit of guesswork. The uncapped off-peak single fare is just £10, so you would not have been charged more than £20. However, it looks like the single from Slough to zone 3 is £5, with the zone 1-2 cap at £8.90. But that extension fare is expensive when you realise that Slough to Ealing Broadway off-peak is only £4.50.
I am slightly more interested in your throwaway comment about being charged twice. Have TfL admitted they claimed the fares twice, or have you queried it with your bank? I wonder how widespread it is.