Without seeing your actual implementation, my assumption is that your Freeform table isn't taking the sequence into account in your columns.
In a fallout, Step A must happen before Step B... Step A and Step B must happen (in that order) before Step C.. and so on...
But generally, when people make a table to represent their steps, they just look at A, B, C, etc in isolation. They forget to build in the sequential logic, hence why the numbers don't match up.
Now, if you have done this, it's possible that your % between steps calculation isn't quite the same?
Sorry, it's hard without seeing your visualizations, segments and calculated metrics.