I seem to be having a similar issue. None of the apps in cloudron are using enough cpu to even show up here, but I am constantly needing to reboot the cloudron vm to get the cpu usage to drop back down to normal levels.
Not sure if you can tell from the graph, but I've needed to reboot it 3 times in the last month because apps become unresponsive whenever this happens.
htop won't help now because it was just rebooted yesterday and everything seems to be running smoothly.
Does anyone have any suggestions on how to find out why this is happening, or how to find out the cause?