Likely it's because the application your trying to remove is refusing to let it's services die gracefully. The trick I use involves
ROM Toolbox and works for most applications including the last time I had to uninstall YouTube. I'm using the paid version so some features described my not be available in the free version.
If using ROM Toolbox, then click the applications manager within it and select
Freeze before selecting
uninstall and the application will be forced to quit and not able to start again. However, do be sure to make a full backup of your whole phone either though custom recovery or ADB because if you freeze some applications (other than YouTube) it'll cause your phone to barf or bootloop until restored.
Additionally some applications will still have some hooks still running after uninstall so reboot to have that flushed from memory.
Lastly don't go using this freeze ray trick on system applications because that'll often cause bootlooping and other issues. If you do freeze system applications and the device still operates then don't uninstall the frozen system app because this can also cause bootlooping when system integrated apps try to access the uninstalled app.
Apps I know cause issues (some more than others) when frozen are; stock messaging, play store & service, phone application (even on tablets), clock and system; don't ever freeze the system or UI app unless you like restoring from backup.