There is no way for a program to know that you are inputting the same enties, as you could have more than one brokerage firm. There may be an instance where the download doesn't work and you have to manually input.
If you haven't e-filed, delete all your manual entries, after making sure the download is correct. Check your prior year returns against your hard- copies and amend if necessary. The IRS is backed up and it takes them a while to catch up.
