Yes they are quite common. Infact they can end up being much greater in my experience.
I checked a gun with two different Chrono's at a site once and there was over 100fps difference.
There can be many reasons for the difference in FPS reading, there could have been issues with the gun, or any number of issues with the chrono itself including low batteries giving artificially low readings. Chrono's becoming damaged during use, for example bbs striking the sensors.