First question, are you on a stock rom or a custom rom?
Second question, what did you use to install the apps?
The reasoning is quite simple tho, the main principal of rooting is giving you access to the files and data at the root of the device. Since you now have unrestricted access to any and every file, things get added in the system partition. The system partition doesn't get fully wiped when doing a factory reset. Just restores to default values. Thus any app that may have been added in the system partition will survive a FDR.
Prime example, this is why you can not just unroot your device by a FDR. SU will still be there because it's in the system partition.