Tnx cmstew!
The emails are coming randomly without any connection to what i see on the logs or the time the jobs are starting to run.
And nothing special found on the logs, Just the jobs running … 
May 23 06:00:01 host CRON[9838]: (admin) CMD (sudo /usr/local/hestia/bin/v-update-sys-queue backup)
May 23 06:00:01 host CRON[9839]: (root) CMD (/usr/local/maldetect/maldet --mkpubpaths >> /dev/null 2>&1)
May 23 06:00:01 host CRON[9840]: (admin) CMD (sudo /usr/local/hestia/bin/v-check-disk-band)
May 23 06:00:01 host CRON[9841]: (admin) CMD (sudo /usr/local/hestia/bin/v-update-sys-rrd)
May 23 06:00:01 host CRON[9843]: (admin) CMD (sudo /usr/local/hestia/bin/v-update-sys-queue restart)
May 23 06:02:01 host CRON[10328]: (admin) CMD (sudo /usr/local/hestia/bin/v-update-sys-queue restart)
May 23 06:04:01 host CRON[10433]: (admin) CMD (sudo /usr/local/hestia/bin/v-update-sys-queue restart)
I found another thread about this issue in the forum and there is no clear answer how to fix this. 