I'm experiencing the same. My sim will bypass 5 open kitchen counters to go to the upstairs bathroom counter to cook. I put stuff on the bathroom counters thinking that would stop them because it's blocked, and they still do it. It's annoying.
Absolutely STILL happening... whether or not I have MODS installed. I remove my MCCC and TOOL mods and it STILL happens. I know there is space on the counters by the stove to do the job in, unblocked (there is nothing on them or above them). So, I don't understand the path logic.
