From the line numbers you mentioned, it sounds like the taxable amount for an SSA-1099 for Social Security benefits was not correct (line 6b). If you had Federal Tax withheld on your SSA-1099 this may have populated the amount in Line 25b.
Click this link to make sure your return was actually filed. Did you receive an email saying your Efile was Accepted?
If you determine that your return was not actually filed yet, you can go to the FILE section and complete the Efile process.
You may want to check your entry for Form SSA-1099. Here's How to Enter Social Security Benefits (SSA-1099).
If you determine that your return was actually filed incorrectly, you will need to Amend your Return. However, an amended return does not 'catch up' to your original return and correct it. It's processed separately and can take 12-16 weeks to process.
If that applies, go by the original Amount Due. Once your Amended Return is processed, the IRS will refund any extra amount you paid (with interest).
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