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We have this exact same problem and have just started feeding at 10 pm so it does not work it's way through till morning. It has worked so far ! We used to feed early but apparently this can make it more likely for night time poo and wee. We feed most of the daily food in the mornings and a smaller meal late at night. He goes out after the night time meal in the garden.
She came to us a few months ago having never been outside so in effect trained to wee and poo indoors. It's taken a while but for the last couple of months she's been fine during the day but we still wake up to a wee and a poo every morning. We let her out before we go to bed at night and she runs outside does a wee and comes back in so she appears to know what she's supposed to do and she has out other dog to copy. I've tried making her last meal fairly early ie 4pm but its not making any difference.