What Are the Possible Side Effects of an Eyebrow Transplant?

Eyebrow transplant has similar risks to other hair transplant procedures, such as bleeding, infection, numbness, and scarring, but all of these are very uncommon. Other risks would include mis-alignment or improper orientation of the hair shafts, in-grown hairs, graft failure, damage to surrounding natural brow hairs, and mis-match of hair color or texture. Additionally, it is important to remember that the transplanted hairs will require regular trimming once they begin to grow.
All the best,

Hello,If you continue to pluck your eyebrows, your eyebrows will be overly thin.  Hair transplantation to the area is a great option. 
Eyebrow transplantation takes a special set of skills.  We are unique in the sense that we will do off-label use of ARTAS for eyebrows to get quality grafts for transplantation.  The key with eyebrows is to ensure that the implanted hairs follow the natural direction of the eyebrow.  Best,Anil Shah

Having performed over 400 of these eyebrow transplant procedures, I am confident in telling my patients that there is a very low risk from these procedures.  Patients need to understand that not all of the hairs regrow in some cases, however it is quite easy to further transplant more hairs if this should occur to achieve greater density.  Typically 15% of the hairs do not grow in the ideal direction in which they were originally transplanted, which means they may need to be plucked or trimmed.

To address your concerns, there are rare few negative long-term side effects of eyebrow transplant. With the follicular unit extraction method, scarring is minimal and donor hair selection is optimal. It is possible for the pre-existing eyebrow hairs to fall out temporarily due to lack of blood supply during the procedure. But in the off-chance that this does happen, these hairs will grow back. One of the main side effects that everyone must deal with is the growth rate of implanted hair. Usually taken from the back of the head, donor hairs will continue to grow to their innate length, which requires occasional trimming. This can be avoided with the use of leg donor hair via body hair transplant.

Definitely trauma to the existing hair is a possibility.  The hair that is transplanted can grow and can require constant trimming.  Also, if hair on your head doesn't match eyebrows it can look very abnormal.