Tax Exempt Interest

I have 2 issues related to reporting tax exempt interest.  First, I have interest reported on Form 1099-INT Worksheet.  The amount correctly carries to Schedule B, Box 8.  But it does not appear on Form 1040, Line 2a.  Line 2a is blank but clicking through ("goto supporting form") shows everything is apparently connected or linked correctly.

 

The second issue is also with the Form 1099-INT Worksheet.  On my Form 1099-INT, Box 13, Bond Premium on Tax-Exempt Bond, reflects an amount of about $5000.  However, I am getting an error message that says the amount in Box 13 of Form 1099-INT Worksheet must be reduced to the amount reported in Box 3 (should be Box 😎 of this Form 1099-INT which was about $3000.  Continuing, "any excess amount is a nondeductible loss".  I can certainly override the amount in Box 13, but is that the right step to take?  And, what about the delta of $2000.  What happens to it?