All my phals have developed discoloration like that on some of their roots - I always assumed it was because they were parts of the roots that were too exposed to dry air for a little too long, repeatedly. It seems to be more of a problem on older roots than newer ones, but I'm not sure if it puts much strain on the plants - they've got lots of roots without any damage like that, and they've all put on plenty of new growth over the time I've had them.