It depends on why they are using it. What is their subspecialty?
Coding 29999 when it is appropriate is not cause for concern. However, these have to be tracked and monitored before and after the claim to make sure they are correctly reported, covered, and there are requirements to send op notes, FAX PWK (Medicare) and other issues that come up with this. Usually payment is delayed as well.
Some orthopedic providers may be highly specialized in a certain area such as hip arthroscopy. There are some procedures which have no CPT code and 29999 would be expected. In this example, psoas release, glute repair, and capsular plication would all be unlisted. Now, some of those may not be separately reportable with other hip scope codes (e.g.; 29914, 29916, 29915) or may be considered incidental to a greater procedure or experimental.
There are also "newer" procedures being done on other joints that may not have a CPT code.
What a provider should not do is use an unlisted code when there is a CPT code established for the procedure, to get around the fact that they don't "like" the reimbursement for an established CPT, or to unbundle parts that would normally be inclusive to other CPT.
Also, only one unlisted code can be reported per anatomic area per operative session.
There are many open orthopedic proedures which might require an unlisted code as well. You have to work with your provider and practice to establish a policy and procedure for this. If they have a practice which will require high usage of unlisted codes, a procedure needs to be in place. In some cases, this might even mean working with payers ahead of time, and creating fees and code sets within the practice management system so they get coded correctly.