This is not a design flaw. At a current draw of 0.02 mA, the Steripen will take about 8.5 years to exhaust a pair of series-wired 1500 mA/h capacity CR123 cells.

1500 mA*h / .02 mA = 75000 hours or 8.56 years.

What brand of batteries are you using in the Steripen? I read a discussion about the variance in inexpensive Chinese CR-123 cells that were brand new. Using a lithium battery charge meter the author determined that in a batch of 64 cells, 1 out of 6 measured less than 20% of capacity. Maybe you got a lemon.