How much you wanna bet someone engaged a bypass because of the problem closing the door. Thinking they got it secure... but maybe sensor wasn't showing... so they engage bypass. Then... later.. door pops open. It's possible the new control system didn't implement the operating with bypass the same as the old system.
This is probably a training/policy failure more so than having 3-4 system failures. Policy failures like running the train with passengers in a cabin that had the safety system bypassed... etc.
As someone with a bit of unfortunate insight into amusement park mishaps and the mechanics (pun somewhat intended) of how they work, you are most probably correct in your assumption. The vast majority of accidents at parks are directly attributable to human error. Of those, that majority is usually then related to times when operators or maintenance manually circumvent safety measures or established practices.
Without providing the usually gruesome details, most tracked ride collisions are attributable to someone overriding the automation and running things in a manual mode.
Case in point... the last time the WDW monorail fleet made national news.
The accident at the TTC was caused by the nighttime parking operations of getting the fleet transferred back to the barn. During this time, the normal automation is circumvented because of the need to transfer to the spur line and unfortunately a series of bad events resulted in the tragic accident.
While we don't know what caused the door to either open while the monorail was in motion yet, I can guarantee that the first place the investigation will start will be with the last time that door was brought under scrutiny (which was likely just before it headed out to EPCOT based on the accounts of the passengers if someone was working on the door). Whether it was someone overriding a sensor intentionally or it was simply a failure, if the door was just inspected prior to departure and that departure was delayed and required Cast Member assistance to resume normal operations - a checks and balance system should be in place to make sure that RV was ready for guests and that should include a maintenance sign off and likely complete test cycle to ensure the issue was resolved. There should be a log of who did what and when it was last checked and that will likely be very helpful to the investigation.
I know that I've had the thought of "what if" and those doors go through my head many times on a crowded monorail when you get jostled into them while standing.
The good news is that nobody got hurt and there is still time to fix the underlying issues with the monorail fleet. The real problem of the age of the fleet has to be addressed at some point. Maintenance hours have been reduced in manpower, then increased in curtailed service hours to the line; but, there is only so much you can do to stop the need to eventually replace an aging line. The amount of maintenance they need will only increase over time and during a time when the hours they are needed to be in service continue to increase.
For this incident, they won't be so lucky as to simply close off the "increased risk" cabins in question to make the problem go away.