This bug has been affecting me for about a week now, I think. The issue is that when I am catching fireflies, the location that the fireflies fly to when I put out the jar is not actually where the jar is; they fly a bit to the right of it. On my 19" monitor, this distance is about an inch.
I've adapted by opening my jar up about an inch to the left of the swarm, and they all fly down into nothingness and get caught right away. Also, this bug seems to make the "catch counter" flakey, sometimes it will count the first few, but not the rest of them.