If an individual's adjusted net income
(net of pension contributions and gift aid donations) is more than £100,000 in a tax year, then the personal allowance is taken away at the rate of £1 for every £2 of income over £100,000. For 2013/14, the personal allowance was £9,440 so it would all have been lost if the tax adjusted income was £118,880 or more.
From the figures you have given, your husband's adjusted net income for 2013/14, assuming that is the year you are dealing with, was over £118,880 so he would not have been entitled to the personal allowance for that tax year.
Your husband would have paid his personal pension contributions and gift aid donations net of basic rate tax relief at 20%. The tax office would have paid the 20% tax relief on the pension contributions to the pension plan provider topping up the contributions to 100%. The 20% tax relief on the gift aid donations would have been paid to the relevant charity or charities.
Given that he has already had 20% tax relief for these payments, in order to ensure that your husband does not get more tax relief than he is entitled to for the pension payments and the charitable donations which would be the case if they were simply deducted from his income before the tax was calculated, the gross payments are added to the 20% tax band so that an equivalent amount is not taxed at 40% or 45%, thereby effecting the higher rate tax relief. Therefore, the 20% being charged on the self-assessment is covered by the tax relief paid to the pension plan and the charity or charities.
I hope this helps but let me know if you have any further questions.