Yes, shouldn't be stored in close proximity...but in a cool, dark place with air able to circulate around them (both onions and spuds). Plastic boxes and bags not a good idea...unless it's small new spuds in the fridge for several days.
I have last few of my potatoes in strong paper Catsan bags, very useful. I just have to remember to chit them occasionally. Onions are hung in dark shed. Lasting very well.
I didn't know they weren't meant to be kept together. I try to keep my potatoes out of daylight in a canvas bag to stop them going green, and usually just put the onions in as well.
I'll keep them separate in future.