What are the potential pitfalls of having a PhD?
Though a Ph.D is not necessarily a disadvantage, depending on the field and the nature of the Ph.D, it may also not be as competitive as the equivalent number of years in industry.
Think from a perspective of a hiring dev team leader who needs a good systems engineer yesterday to help integrate some obscure API from a vendor into their product. You're choosing between a pile of resumes.
On one, you have a candidate who has 3 years as a junior engineer in a company that worked on image sensors, 2 years of work as a systems developer II, and one year as a lead developer on a computer vision project. He's delivered seven projects in total and has worked in a highly cross-functional team of hardware and software engineers, salespeople, and on-site support staff. The products he worked on brought the company revenue of $86.3 million dollars over seven years.
On another, you have a candidate who has done 6 years in a Ph.D and 1 year worth of internships in total. He's worked on a computer vision project and has contributed a novel algorithm to solving "Line tracing under low UV light conditions" (I made that up, I have no idea if that's a real problem in computer vision), and has written six publications. He also has taught a course on 3rd year systems programming and has TAed robotics three times.
While they are both good candidates, chances are that unless you need someone who does "line tracing under UV light", the first candidate might be more attractive. Less training, less having to work with that person to integrate them into a product-based flow, proven record of delivering product and making sales, etc...
I personally feel that the "disadvantage" of a Ph.D is more about opportunity cost than an actual disadvantage. In many cases, the culture of academia vs. industry are different enough that it's like switching fields even if the technologies are similar. Basically, someone with 7 years actual work experience has enough to basically go from a new grad hire to a project team lead, whereas someone with 7 years of Ph.D is proven to deliver in an academic setting but not in a for-profit product-based one. However, at the same time, there are many industries that want to have Ph.Ds on their staff as well because they are long-term, deep thinkers who are rigorous and detailed.
In my field (bioinformatics, systems/computational biology) if you don't have a PhD you practically don't exist on the map, but yet it's a very research oriented field.
I can imagine a couple of issues where a PhD might have a negative effect on the attractiveness of a candidate, while none of the below are prove-able facts, they are directly based on my experience (myself, people I know, etc.)
Overspecialization: In many industries being overspecialized might hurt more than it helps. You might get stuck on obscure case scenarios, or obsess about rigor before anything else. Likewise doing research might have an effect on having a more abstract, rather than practical, way of thinking. Most of us don't really "deliver" a product.
Jadedness: Those 4-6 years spent doing research is likely to have caused some self-doubt, questioning yourself. In my experience most people that go corporate after uni live in a state of blissful ignorance, compared to their classmates who've gone on to pursue PhD studies. (yes, I might have exaggerated it a bit but the point is still valid I believe)
Attitude: While this might not be the general truth, in my experience people in the academic world is much more laid-back than corporate world. While most of my old classmates are expected to be at their desk at 7 or 8 sharp, and expected to leave latest by 5 to avoid working overtime, I can practically show up and leave whenever I feel like. What my boss cares about is whether or not the project progresses as we have decided. A potential employer might be wary of such "bad habits".
As I said, not a factual answer but I hope it provides some insight, anyways.
An important issue associated with having a PhD is that many "traditional" routes into industry are effectively closed off.
For instance, a chemical engineer with a bachelor's or master's degree could take a position in just about any corporate division of a major company—they could work in production, sales, research, or just about any other field, with corporate training providing the requisite skills needed to do the job. By contrast, someone who holds a PhD will simply not be considered for these positions, as they are too specialized, and too far above the requirements for such a position. Any hire into such a position would probably not offer a sufficient "return on investment" to be worthwhile.
It would also be difficult to cross-train for "standard" management positions, as while a PhD does offer some supervisory experience, it's more useful for research-based organizations than industrial positions.