construction costs escalate much faster than inflation. Last year saw costs increase by almost 15% IIRC - mind you that is well above normal, but 5% annual increases is pretty standard.
The accounting change only reflects the increase from $2 to $3.2 as well - other cost increases are attributed to scope creep. The scope creep mostly comes from the city doing land use planning studies for STC and realizing the kinds of spending required in the area that can be bundled into the subway project (road reconfigurations, public realm improvements, etc.).
If you compound a 3.7% annual inflation rate to 2026 from 2013, $2 billion becomes $3.2. It's not that crazy.