You will likely not see oscillations with a scope in case of floating digital line. The reason is that probe itself will likely be enough load to pull it down and stop it.
Again, I'm not saying that floating pins is for sure your problem, but seems worth checking. You will not believe how strange it may act. It might be totaly unpredictable, there are leakage currents inside IC, also PCB level leakage currents (like someones fingerprint, or soldering flux leftovers) it may react to humidity, external EMI and so on. So the line may randomly transition in logic states, hang in the middle causing increased consumption, or randomly wake up MCU if it has interrupt attached. So it would theoretically fit your description, that some boards are affected and some not.
Unless your firmware is very complex, it sounds strange that 5% is affected and others not. Typicall, firmware is quite deterministic.
I quickly looked your schematic. Noticed, that you do not have pullups on CS lines. Generally, you should have, because while MCU is in reset, they become undefined (this is not likely to be related to your problem). What can be related to your problem is STM32 MISO line, because if no CS line is activated (bus is not used), then it is tri-stated (floating). So check that you have pullup enabled on this one (in firmware).
Also, I see you have interrupts attached to accelerometer? Maybe it causes MCU to wake up?