Pages 8-11 of the BIS 1996 paper on backtesting provide very useful general guidance:
Hope this helps.
Many of these (positions mismatch, risk factors not captured, parameters not updated or calculated incorrectly) are as applicable to historical VaR as to any other VaR calculation approach.
In terms of the solution, in addition to the length of the observation period that you mentioned, one can also look at volatility scaling, improving the accuracy of the valuation, brining in additional risk factors etc. Understanding the causes is therefore very important when devising an improvement plan.