Based on the information provided, it appears that the problem could be due to any of the following factors:
- Weak/Dying Battery: Can be verified by changing the battery
- System not going to deep sleep: Could be due to wakelocks letting the system alive either from apps or system like media server. Clean Master may say that it had killed apps, but it cannot kill apps completely , including background processes unless it has root capability and is designed to do so. Neither does it ask for root permissions nor does the app description claim it can kill background processes, so one cannot trust that it is really killing your apps
I would first suggest that you do a factory reset after taking a back up of your data. I am presuming your device is not rooted, so you can see this for taking a back up Full Backup of non-rooted devices. This solution does not cater for SMS, contacts/ calendar which can be done using CM backup
Instructions for doing a factory reset for your device here. If the problem persists after factory reset, then I would suggest you to change your battery.
I am hopeful that this should resolve the problem. Please revert with Irvine and edit your question with additional information sought in the comments section, which would come in useful if the problem is not resolved
Coming to your other question, leaving it on charger overnight is not recommended, since the Battery gets internally hot and stress caused by this reduces battery life as you can read Find out how to prolong battery life by using correct charge methods.
. Related inputs for additional reading Should I charge phone overnight or let battery down to a minimum?
Are you on MUI 220.127.116.11? Asking since rapid battery drain seems to be a problem , unresolved till mid last year, as per reports here
In any case, your device has the facility to identify battery consumption separately for hardware and software (app wise) as shown in screen shot below taken from the same source. Can you study that to identify the culprit, in case of rapid drain? You can quickly weed out the battery hogging apps using this