Hopefully, this helps someone else.

I had this exact issue today and it was driving me nuts, then I figured out what I was doing wrong. Let me explain.

I was hand entering the last couple of entries for the month. When I entered and split a Walmart withdrawal, it also created a deposit. I was like WTF... 

I have an entry in Quickbooks called Personal, for all things personal, but in the last couple of months I moved personal under one called "life"

So the issue was, when I was categorizing one of the split entries as "personal" ..it defaulted to "Personal checking" (because it was under "life" now,  when before it would default to just "personal" ) which was the exact account the withdrawal was coming out of.

Once I changed it from personal checking to "personal" (which it should have been in the first place) it entered into my register just fine with no duplicate being created as a deposit.

So if it's happening to you, make sure you didn't start accidentally entering the account it's already in, instead of the category you meant to put it under.