I want to use section A of an LM358 OpAmp to limit the current and section B to convert Arduino PWM to analog, and then connect output B to non-inverting input of input A as reference voltage.
The LM358 VCC is not going to be lower than 12V or higher than 16V.
Is there something like "leakage" of current/voltage or anything else between two sections that can damage the Arduino or two sections are isolated from each other?
There is a very slight interaction between the two amplifiers at low frequencies that is likely equivalent to a few uV of Vos shift.
That is in part due to the shared bias network. Changing dissipation from the output section of one amplifier can cause temperature gradients across the die as well has heating, as @analogsystemsrf mentions in a comment, which will cause Vos changes in the other amplifier.
If both amplifiers are working with signals measured in volts it won’t likely be noticeable, let alone problematic.