System wakes up automatically several times during sleep (logs says RTC Alarm) and improperly Ejects external HD. [MBPro Late 2012 + OSX Yosemite]

Question

Hi there,
Background:
the main issue is that after system wake-up I find often several notification messages about my external drive not being properly ejected.
This seems to be a common issue for many Yosemite users, some say disabling Spotlight indexing for that volume solves the problem, but this is not my case. That's why I'm creating another thread.
Multiple ejects:
Looking at system logs it comes out my MacBookPro with Yosemite when put in standby is actually waking up several times every approx 90 minutes to do something.
(MBP Late 2012: not a new MBP with PowerNap and thus cannot use nor disable it)
Logs are like this:
20/02/15 03:21:13,000 kernel[0]: Wake reason: RTC (Alarm)
20/02/15 03:21:13,000 kernel[0]: RTC: Maintenance 2015/2/20 02:21:13, sleep 2015/2/20 00:33:19
20/02/15 03:21:13,000 kernel[0]: Previous sleep cause: 5
20/02/15 03:21:13,000 kernel[0]: AppleThunderboltGenericHAL::earlyWake - complete - took 1 milliseconds
20/02/15 03:21:13,062 sharingd[235]: 03:21:13.062 : SDStatusMonitor::kStatusBluetoothPowerChanged
20/02/15 03:21:13,000 kernel[0]: TBT W (1): 0 [x]
20/02/15 03:21:13,000 kernel[0]: [0xffffff8050811400](0)/(5) Device not responding
20/02/15 03:21:13,000 kernel[0]: disk3s2: media is not present.
20/02/15 03:21:13,000 kernel[0]: disk3s2: media is not present.
20/02/15 03:21:13,000 kernel[0]: disk3s2: media is not present.
20/02/15 03:21:13,000 kernel[0]: disk3s2: media is not present.
20/02/15 03:21:13,000 kernel[0]: disk3s2: media is not present.
20/02/15 03:21:13,000 kernel[0]: jnl: disk3s2: do_jnl_io: strategy err 0x6
20/02/15 03:21:13,000 kernel[0]: jnl: disk3s2: end_transaction: only wrote 0 of 32768 bytes to the journal!
Questions:
- What is WAKE REASON - RTC (ALARM) ? - Could it be linked to Auto Time&Date Setting?
- Why disk3s2 is not present?
Disk is badly ejected only when connected through USB hub. When left connected to MBP USB port seems to behave fine.
Before Yosemite I've never had any problem with external HD connected to the hub.

Answer 1

I believe this is ready for submission for the Time Machine forum.
As noted, it does not cover diagnosis and correction of specific problems or errors, as that would seem to be better handled separately.
It also doesn't cover anything about Time Capsule, for the very good reason that I'm not familiar with them. If someone wants to draft a separate post for it, or items to add/update here, that would be great!
Thanks very much.