What time in the morning did you check up on the SEP client?
Like what Fatih said, you may want to modify the scan behavior from the server.
I'd like to expand on this: go to Policies > AV/AS > Select the policy and rt-click edit...
Go to Administrator-defined scans > select the schedule, click on edit >
Schedule tab. I suggest you untick the 'Missed Scheduled Scans' if your client frequently misses scans.
Also, I suggest you change the scheduling of full scan from daily to 1/week. You may want to create an Active Scan instead which is a lot faster and takes less resources. Or, create a custom scan to scan specific directories most likely to host malwares during office hours.