For the most part, yes. Vegetable cookery tends to happen at temps north of 175, and protein cookery tends to happen at temps south of 140 or so, so you can't really use the same unattended water bath for both.
I typically do the veg in bulk for the week and ice bath->fridge them, then reheat in the water bath while I'm finishing the meat, but yeah, it wouldn't work to do simultaneously (unless you e.g. wanted traditional-texture braised meat, which works quite well in a veg-temp water bath).
