I assume wake homing isn't perfect (otherwise everyone would do it). It does provide a very stealthy and hard to spoof attack.
If you miss identify your target you may fire on the wrong location (or do what I did once - fire a weak homing torpedo at a helicopter
)
There is also the danger of your torpedo being slightly inaccurate and passing in front of the enemy (rather than behind - where it can find the wake). So, the best scenario would be to calculate the firing solution yourself. I can't be bothered so I usually attack from the stern or the bow (as this largely solves the problem).
Note also that - even if the torpedo acquires the wake - depending on the angle there is a chance it will turn in exactly the opposite direction of what it should.
Finally - I tend to set running depth to 20 metres (as I believe this is the listed acquisition depth - although the game default/AI selected values is a deeper depth ...well below the wake).
I hope that helps.
Good hunting