Yours is the first report I've seen saying the Senior Deduction was too small or was it completely missing? Maybe they reduced some income and your AGI? These are the only things I know that can affect it. Probably the second item.
Check your date of birth under My Info
Check that your ssn under My Info wasn't marked NOT VALID for employment.
If you are married you have to file a Joint return not Separate
For Single the deduction starts to phase out at 75,000 and maxes out at 175,000
For Joint the deductions starts to phase out at 150,000 and maxes out at 250,000