This sounds like a paper work / bureaucratic failure rather than an engineering failure.
I'm no expert, but I'm pretty sure that the 787-9 could have landed and unloaded its passengers just fine. However it likely breached 'pre-certified' criteria or similar regulatory requirement. Most of us engineers bump into similar rules or codes. We know something will work, but it isn't in the rules so it isn't allowed. When it comes to commercial aviation it makes even more sense to have strict rules.
Last month the plane I was on left the terminal and was almost onto the taxi-way when it had to return to the terminal for "paperwork reasons". It seemed ridiculous, but the systems are in place for a reason. In this case it was probably caused by a family that almost missed their flight so PAX and weight of the submitted paperwork might not have been accurate.