I've read about many users who updated to new firmware (v6.40.5 [current]) were having their devices stuck in boot-loop or worse.
Can someone, preferably from MikroTik devteam, tell me what was the root cause for that?
What precautions can\should I make to ensure safe and error-free update?

I just did that this afternoon. It is wise to wait a few day to see how the early adapters are managing.

Make your backup of the configuration and manualy also the 6.40.4 firmware on your pc so have it ready to use or revert to later.

I've read about many users who updated to new firmware (v6.40.5 [current]) were having their devices stuck in boot-loop or worse.
Can someone, preferably from MikroTik devteam, tell me what was the root cause for that?
What precautions can\should I make to ensure safe and error-free update?

U upgraded to 6.40.5 without any issue. Working as should be. No problems at all. All works perfect ! RB750Gr3

I needed to send one rb750gr3 to RMA because of boot loop and because I was not able to initiate a netinstall. Other devices of this model went good.

Its happening, but because you say that only one unit is affected them is nk reason for panic. This update works ok kn my unit.

I needed to send one rb750gr3 to RMA because of boot loop and because I was not able to initiate a netinstall. Other devices of this model went good.

That's a bummer. I really don't want to trigger whatever bug is affecting updates. Did this happen with updates in the past? IMO this is serious issue that should be investigated.
This kinda speaks a lot about quality of firmware, at least because of multiple reports from different users in this thread viewtopic.php?f=21&t=127485.
I can't imagine going through netinstall procedures, being unable to use full backups of configs, etc, if I had multiple MikroTik devices installed for my customers...

Just to add. The boot looping device was upgraded by direct download an install option. Hope it is on the way to mikrotik company through the distribution channel so they can investigate. All others was updated by copy-paste of predownloaded packages and reboot.