You know that's an interesting question. What we know about hominin stress periods comes mostly from small deficits of enamel formation on the teeth, called hypoplasias.
For example, here's a photo of lower canine tooth of Homo naledi that I took in the lab today. You can see two linear enamel hypoplasias as parallel "stripes" low on the tooth crown. 
Those two hypoplasias represent periods of a couple of weeks during which the enamel didn't form with the same strength and rigidity. That reflects "developmental stress", which could be malnutrition, or acute severe disease, or other stresses.
Because these reflect times during tooth development, we can work out the ages of individuals. Needless to say, this tells us a lot about stresses on children, and little about adults.
Hypoplasias and other stress markers are more common in some human populations than others. They are most often found in populations with food insecurity and high rates of childhood epidemic diseases. They also accompany weaning stress, especially to low-protein foods like maize.
Some archaic human populations had a lot of hypoplasias, especially Neanderthals. We've long thought this was an indication of dietary insecurity, although today we are revisiting disease as a possible major factor.
Living and fossil non-human species also have similar enamel defects that reflect developmental stress. Here's a Sivatherium (ancient giraffe) from the Miocene of Pakistan! dx.doi.org/10.17582/journ…
Heck, when you're investigating fossil fauna, you may even be able to dissect out erupting teeth to check out their hypoplasias, like on this Miocene rhinoceros from Nebraska! doi.org/10.1080/027246…
So plenty of other species manifest developmental stresses in the fossil record. Skeletally very little can tell specifically whether malnutrition was the source of stress; no fossil hominins exhibit the kind of extreme wasting that some malnourished people do in recent times.
Another indicator of developmental stress is the occurrence of "Harris lines", which mark an interruption in the development of bones at the growth plate. (image: Wikipedia)
Neanderthals also had Harris lines sometimes. For example Shanidar 10 is a juvenile tibia from Iraq, and Libby Cowgill (et al. 2007) showed the Harris line formation:
But interestingly, we have only rarely noted Harris lines on fossil hominin material. This may just be because the numbers are so small of adolescent and juvenile long bone hominin fossils. Bone remodeling often eliminates these lines in adults.
