Yup, they sure can, much to all our chagrin. Here's an interesting exploration on the why's and how's of this phenomena, from a guy on eTurbo News with two knee replacements and an unfortunate and unexpected change in seat assignments. A snip:
With variations among the same narrow-body family of planes, such as among different 737 variants, different Airbus 319-320-321 variants, 737-757 changes, or even Airbus-to-Boeing changes, seat mapping is generally consistent: C and D seats are always aisles, and such. But even within these families, direct substitution is sometimes not possible. For example, some Continental models do not have row 11, some others do not have rows eight to 15, so if your initial assignment is in one of those rows, you can't keep those same seats in a switch.
So, there is a method to the madness. But we still don't have to like it (especially claustrophobes like me who go nuts when stuck in a middle seat).
For more offbeat airline news: Canada Gives Obese Fliers an Extra Seat for Free. Wherever you stand or, er, sit on this one, ramifications from this ruling may be coming to an airline near you.