I have connection like on the screen I have 12 arduinos. Each of them has one general 12V power supply. The problem is when i connect one of the Arduino supply (while all scheme works) Raspberry pi i2c pins burns. Already 2 broken raspberry. I guess it because the supply jack connect "plus" at first and then "minus". So while we have "plus" connected, the electrons run through i2c connection to the "ground". Please, help to resolve this. Thanks!
I²C is open-drain (NOT tri-state) and you can safely connect devices to the Pi (regardless of their nominal operating voltage) provided it does not have pullups to 5V - which AFAIK is the case for the Arduino. Open-drain can ONLY pull the voltage to Gnd - the only supply comes from the pullup resistors.
BUT the Pi output voltage levels may be marginal so it is a good idea to use level shifters; I have used the Pi with many 5V devices using I²C without level shifters.
There are however errors in your wiring. I²C requires 3 connections; SDA, SCL AND Gnd. You should directly connect the Arduino Gnd to the Pi Gnd and not rely on a tenuous path through the power supply.
It is also inadvisable to remove/connect power to a device which is connected to the Pi (or any other circuit).
The state of the Arduino pins will be indeterminate during boot. Most devices initialise as inputs, so should be safe, but there are no guarantees.
There are better ways of interfacing to the Arduino I²C is a poor solution - it is designed for short range on-board communication.