Unfortunately i have no answer here at present just questions and some observations
The hard copy calculation arrives with a comment and the marriage allowance deduction removed.
What did it say comments wise?
are you 100% certain the spouse has transferred the allowance and that this has been processed onto "your" account awaiting the calculation? - hmrc should be able to confirm
Without a processed transfer application from the spouse the claimed amount will always be removed
D&C is spot on with the dividend comment - i have run test calcs on my package and £1 of dividend income above h rate removed the marriage allowance even if that divi is within the Nil rate of tax (dividend allowance)
However strangely this does not happen if the interest received figure is less than £500 but pushes the income over the adjusted h rate level.
I am guessing my tax calc package is correct but anything is possible nowadays in this regard.
How should charity donations work and is the marriage allowance due?
Charity donations should work extending the basic rate band - if its a divi/interest received subtlety full details of all relevant income sources and gift aid relief may be needed to give the full answer - (once someone who knows the full chapter and verse is able to comment too
relevant note - its probably? too late here if the return has been submitted but the ability to carry back following years gift aid payments made before return is submitted may help if one has just exceeded the limit and those later gift aid payments carried back may have sorted the issue.