Take on the double endorsed deposit

I made a deposit directly into the ATM to our joint checking account a few days ago and thought nothing of it until I noticed a few days later that one particular check hadn't cleared and the amount had been debited from my account.    I get that there are sometimes delays but this seemed pretty odd as the debit transaction happened only a few hours after the initial deposit transaction.   After spending a good part of a half an hour with a Citibank representative, I was told that since the check was made out to both me and my wife, we should both have endorsed it.     

I've had a joint account for almost a decade and have deposited tons of checks with both our names listed but this was the first time it was tagged as suspicious.  

Can somebody explain the logic behind this?

I can make a withdrawal without having her signature but I can't make a deposit?   Isn't the act of taking money out of an account much more worrisome than adding to it?  Both of our names appear on the account, and checks made to either individual person can be deposited with only one signature but a check make out to both requires two signatures??  The entire thing is maddening.

 

So not only did the deposit not go in when I made the initial transactions but I had to spend time out of my time to wrap my head around the mental gymnastics they asked me to perform to understand the rationale and then it took four days to get the check sent back to my hours which I then had to get double endorsed to bring back to the same bank to re-deposit it.