That might be why it was left in. Though this isn't so obvious, since- as you quite rightly pointed out -not all fowls have trouble flying. If it is intentional and/or well known, then there is no problem. I merely point it out in case it was an error that's been missed.
fall foul/afoul
1. Nautical To collide. Used of vessels.
2. To clash: fell foul of the law.
As with many idioms, alternate spelling and pronuciation can become attached to a phrase. In this example, both have become accepted forms.
On a final note, I'd like to apologize for the lengths I manage to draw tiny points into upon occasion.