This is actually a bit of an annoying problem for us! All the 1040 instructions say to round all figures at the end. So it is expected that you would have a few cases of 1.49 + 1.49 = 3 showing as 1 + 1 = 3.
But the freefilefillableforms supported by IRS rounds all input and then does addition based on that. For now we just maintain all cents and do math with the precise numbers, then round at the end when the numbers need to go into the forms. We have some work in the pipeline now to make that user-configurable too.
The way it seems it should work is that once the amount is entered on the form, it should be treated as the whole dollar amount for subsequent calculations. E.g. if the number comes from Schedule C, once that form is completed and you "enter this amount on line X of Form 1040" then any further calculations on the Form 1040 should use the whole dollar amount as printed, not the dollars and cents.
But the freefilefillableforms supported by IRS rounds all input and then does addition based on that. For now we just maintain all cents and do math with the precise numbers, then round at the end when the numbers need to go into the forms. We have some work in the pipeline now to make that user-configurable too.