Were the structured notes and their hedges meant to have zero P&L? An example of this not being true, the desk has large positive P&L when it sells a note to a client, then during the life of the note, the dessk has negative carry and/or costs of dynamically rehedging. In this case, negative P&L is by design. One of the reasons why the negative P&L is greater than expected might be that the bid-offer spread was greaster than expected, or the market was more volatile, and the re-hedging was more frequent than expected. The lesson learned is to charge clients more in the future.
If the notes and their hedges were meant to have near-zero net P&L, but have non-zero P&L, then, as Kermittfrog commented, a good P&L Explain tool would be very useful. If you're able to attribute most of the P&L to various deltas / gammas / cross-gammas and carry / rolldowns, with minimal unexplained P&L, then you should be able to read off right away what fails to net to zero. Some possible explanations are:
whoever structured this, forgot about some negative carry or financing costs that the desk pays and fails to pass on to the clients
The hedges don't exactly replicate the payoff of the note sold to the client, the desk retained some market risk. For example, they sell to the clients an embedded option with some strike and expiry, but hedge it with options with different strike and/or maturity.
It is also a good idea to look at the VaR. If the VaR is close to 0, but the P&L is not, then the VaR probably needs to be debugged. If the VaR is in line with the P&L, then if you have better than average VaR analysis tools, you can see what market scenarios caused the P&L in the tail, and what market factors drove it.