It happens to me in the following situations:

1.) When flying multiple sectors in rapid succession, and/or mixing the KA/CX fare codes. Weeks where I have 4-8 segments, particularly in rapid succession on complex or jumbled itineraries (ie, ex-Taiwan to mainland China ticket with a stopover in HK, and during the stopover flying a separate HKG-SIN round-trip before proceeding to the mainland). It seems exacerbated when the tickets are a mixed bunch of CX/KA metal and jumbled CX/KA codes (I don't care which code I book under, and often find myself flying CX on a KA code or vice versa).

2.) Changed itineraries - aka, originally booked on (x) date and moved to (x+1) date.

3.) Upgrade-with-miles tickets. Had countless instances of PEY-J or J-F where no credit was issued without calling MPC (sometimes, multiple calls...and multiple rejections..."fare code is not eligible"...sigh).

4.) "M" is printed on your boarding pass. Presumably "M" is for "Manual" seat change, sometimes I've been upgraded for reasons I an oblivious to. It's not an op-up, but "M" seems to mean good news more often than not, kinda like "V" (which I see for birthdays and milestones). Maybe the original seat is broken or something else. But anyway, I've noticed when "M" gets printed sometimes the miles sometimes don't come through. I can't recall for "V".

I think this only really becomes an issue when you fly your pants off, or if you're constantly using miles to upgrade.