ITR 2 online submission

Though it shows total amount in total income but at the time of tax calculation the tax is calculated only over excess amount.

You may also raise grievance for it.

If you have income under head "income from capital gain" only, then deduction u/s 80C and also 87A is not allowed. Deduction u/s 80C and 87A is applicable on income under head "salary " and "house property".
This two head should be with the ITR filer.
In your case, you have income from capital gains, recompute the income.