Do you have the mod https://www.nexusmods.com/fallout4/mods/15608 installed?
That fixed a HUGE chunk of pathing issues for me.
The other issue is some static world objects become invisible to their pathing. ? eventually? always? memory issue? idk. Like the walls at the sanctuary home. They can't find the door.
For that i use place in red and hide metal walls or security walls inside the original static walls. And now they can see them and path correctly!
And stairs! Stairs with railings suck. Put a warehouse misc short pole into the end of the stair railing so they stop getting caught on it.
Basically you have to round off any sharp corners on common paths. Round pots/plants, Round trashcans etc.. Work excellent for that.
Altho anymore i've started designing anything to use the 2platform wood stair or the long wood stairs. those two have no issues at all for movin people around to multiple-multiple levels! Dozens of settlers movin around 4 or 5 levels without issue!