I'm a little confused as it seems Delta has accounted for the issue: they say flights had been incorrectly posted to your account and now have been removed.
​​​​​​The fact that *other* flights you have taken in the past have never posted incorrectly seems pretty irrelevant. If you shared information about the flights that have been uncredited, perhaps we can brainstorm as to whether there was indeed an error in the initial crediting.
I'd also note, though I have no reason to believe this has happened here, sometimes miles are uncredited when the airline discovers there were some shenanigans on the part of the passenger. Is there any reason you could think of that Delta may rightly or wrongly think that's the case here? (If indeed they are in the middle of a fraud investigation , it might make sense that they let you have a negative balance before they make a final conclusion.) Forgive my skepticism, but your post seems very carefully worded to say that Delta won't tell you what was wrong with the crediting of the prior flights -- not that *you* have no idea.