Another place I've seen people wanting to put expansion joints (metallic bellows) a lot is on my rotating equipment, primarily high temperature pumps. When stress runs indicate that high thermal expansion rates exceed piping limits, or allowable nozzle loads on the equipment itself, I've seen expansion joints pop up to solve the problem of movement due to thermal expansion between the pump & the pipe. While not really a problem, it should only be a last resort, as everybody else has stated. A couple additional reasons, bellows style expansion joints near the suction of a pump can cause added pressure losses because of the flow over the convolutions. There's also an axial thrust load introduced because of the annular area between the top and bottom of the convolutions that can exceed nozzle load limits on the pump - a lot of people think these things eliminate all loads, but they can actually cause an increase in loads because of this in certain situations.
Another big problem I have with expansion joints is in installation. Expansion joints, at least bellows style joints, are designed for a specific number of cycles over a fixed range of elongation. For example, a joint might be good for 100000 cycles of +/- 0.25", but only 1000 cycles of +/- 0.5". And axial vs. radial displacement makes a big difference too. I once saw an expansion joint designed for four inches axial displacement, and a quarter inch radial, installed in a system (to accomodate thermal growth of a 80' tower made of stainless steel), and be pulled radially an almost two inches to match piping to a vessel nozzle. Piping wasn't where it was supposed to be, vessel nozzle wasn't where it was supposed to be, but there was an expansion joint, so nobody worried about it, despite the fact the fitters had to use a chainfall to pull the joint into place. It was just a fluke I happened to walk past and notice it before commissioning.
There are places where they're unavoidable, but I've found far too many people say 'just drop in an expansion joint' and forget about it. If you've got one shown on a piping isometric, I'd recommend strongly indicating on the iso the actual limitations of the joint, and if possible even wiring a stainless tag with allowable deflection on the joint itself.