This is from the GrowFAQ. purple stems can be from genetics, cold temps or phosphorous deficiency. I have it in my plants more often than not during veg so don't worry about it unless your plants are flowering and have other problems.
"Phosphorus (P) deficiency:
Figure 11 is severe phosphorus (P) deficiency during flowering. Fan leaves are dark green or red/purple, and may turn yellow. Leaves may curl under, go brown and die. Small-formed buds are another main symptom.
Phosphorus deficiencies exhibit slow growing, weak and stunted plants with dark green or purple pigmentation in older leaves and stems.
Some deficiency during flowering is normal, but too much shouldn't be tolerated. Red petioles and stems are a normal, genetic characteristic for many varieties, plus it can also be a co-symptom of N, K, and Mg-deficiencies, so red stems are not a foolproof sign of P-deficiency. Too much P can lead to iron deficiency.
Purpling: accumulation of anthocyanin pigments; causes an overall dark green color with a purple, red, or blue tint, and is the common sign of phosphate deficiency. Some plant species and varieties respond to phosphate deficiency by yellowing instead of purpling. Purpling is natural to some healthy ornamentals."
