If a fish dies, it's very common for other fish to eat the remains. But they can also hide quite well, so sometimes you think a fish is gone only to have it reappear days or weeks later. Rocks, wood and plants can all provide hiding places. I thought once I'd lost a bunch of kuhli loaches, until I did a big rescape and found them again. Just hiding, they're good at that.
If your filter has no cover on the intake, sometimes fish get sucked up, though most healthy fish are more than strong enough to avoid the intake, some get curious and swim up to investigate and are caught in the filter.
I've had several fish survive going into my AC70, before I got smart and covered the intake, they were all under the media basket, and I didn't find them until I removed it for cleaning.