Yes, Mazen, protoplasts isolation may have a significant effect on hormine contents. One keep leaf tiddue in enzyme solution at least for 1-2 hours or even more, perform several washing with the buffers/medium etc. And all of these steps may have aeffect on hpormone transport/syntehsis.
Of course the plant growth regulators (also known as phytohormones) are affected for plant physiology, and the protoplast isolation trigger several plant hormones synthesis pathways as an answer to those stress.
Then in this case how can we know the effect of a treatment, gene, or a pathogen on the cell level without inducing those injury-related genes/hormones? Few good articles in 2014 neglected this part and assayed protoplast response to hormones or chemicals in their experiment!!