In my non-expert opinion .... yes, it is possible to miss fish on a pass through an area.

They could be "on the move", and just came back to that area when you did ...

2d sonar in 5ft of water, or even the first 5ft of water (in deeper water) isn't going to show you much of a swath of the water column or bottom. A 20deg cone angle only shows a ^ that's 1/3 the diameter of the depth ... and even a 60deg cone angle only shows a ^ that's equal to the diameter of the depth.

In other words, the cone emits from the transducer and V's downward, showing more area as it goes through the water & contacts the bottom. A 20deg cone angle will show a circle of bottom that's ~7ft across in 20ft of water, or 2ft across in 6ft of water. A 60deg cone angle would show a circle of bottom 20ft across in 20fow & 6ft across in 6ft of water. So even with a 60deg cone angle capability, your cone ping doesn't cover much territory of the water column in shallow water (and even less, closer to the transducer). That's just the nature of a "cone" shaped sonar ping.

It is quite possible to "miss" fish that are tight to the bottom, especially if there's "stuff" on the bottom (other than the fish) that could disrupt the signal.

Now, I'm not saying that any of this is the situation in your case .... just that it's possible.

... cp