I would interpret this sentence as meaning "isolated ... from tissue." However, I am not a physician or biologist and I can't say whether one would interpret it differently. What I can do is quote a number of publications that use that phrase:
Apoptogenic effect of fentanyl on freshly isolated peripheral blood lymphocytes.
In this case, the use of freshly tells us that it does not mean "isolated cases."
In this study, we used in vitro isolated peripheral blood lymphocytes as
biosensors to test the effect of hypobaric hypoxia on seven climbers by
measuring the functional activity of these cells.
— Peripheral blood lymphocytes: a model for monitoring physiological adaptation to high altitude.
Since "in vitro" means "outside a living organism," we can also safely assume that this usage does not mean "isolated cases."
Thirteen patients with SLE with active disease, 10 patients with inactive
disease, and 14 controls entered the study. In addition, samples from 10 of
the 13 patients with active disease could be studied at a moment of inactive
disease as well. Isolated peripheral blood lymphocytes were stained for
the lymphocyte subset markers CD4, CD8, CD19, their respective activation
markers CD25, HLA-DR, CD38, and the costimulatory molecules CD40L, CD28,
CD40, CD80, and CD86. Expression was measured by flow cytometry.
— Expression of costimulatory molecules on peripheral blood lymphocytes of patients with systemic lupus erythematosus
Again, this usage cannot refer to "isolated cases." This time because it's being used as an adjective to modify "peripheral blood lymphocytes."
These were the first three results when searching for the phrase"isolated peripheral blood lymphocytes," so I think it is safe to conclude that that phrase will only ever be interpreted to mean "isolated ... from tissue."
If you wish to express that staining was observed in only some of the lymphocytes, you might want to reword the sentence as:
Slight specific staining with the antibody was observed in a small number
of peripheral blood lymphocytes.
If your intention was to say that slight staining was observed in those lymphocytes not clustered together, you might say:
Slight specific staining with the antibody was observed in discrete
peripheral blood lymphocytes.
The definition of discrete from Oxford Dictionaries:
Individually separate and distinct:
"That is, does age affect general ability or does it have discrete effects on individual abilities?"
Be careful not to confuse discrete and discreet.