If the batches are not zero, then the total is certainly wrong.
But this does not mean that it is automatically an inconsistency, if your stock is not reduced with a goods issue then this can be caused by wrong customizing too, or countless other reasons.
Hard to find a starting point as stranger, with a hand on the system a reasonably experienced consultant would know where to check.
You already confirmed that you see all the quantity from your screenshot in MCHB, what quantity do you see in MARD and what quantity in MBEW table?
A screenshot from one of the deliveries from table LIPS could also be something to look at for analysis, like table MSEG for the goods issue.