Here's how I see it...
They said that sometimes variants happen because of choices, like showing up late to work when you weren't "supposed" to, and sometimes they just happen. I think some of the other Loki's just happened. A Loki who was born a woman when he was supposed to be a man, etc.
Think of it like spontaneous mutations. The TVA captures and removes those spontaneous mutations and resets the timeline removing the branch they created from the STL.
The question is why does it take them so long to find them sometimes?