You're reading things correctly, and I actually did a double take to figure out what was going on.
On the first page, there is a column called modifier. That number is entered into the equation when figuring out costs for factories. The industrial expansion in your country outpaced your country's ability to support the factories (via provinces and infrastructure), so the prices went up.
Your trait changes depressed the prices. However, because the modifier is an ungodly several decimal number, the stat sheet rounds to the nearest whole number. If I got rid of the -3IP Private Cost trait, for example, your private factory cost would only go up to 5 IP, not 6 IP.