This has nothing to do with weather conditions or lighting. It has to do with basic statistics: if you are looking for a very small subset of identifiers in a very large pool, and you have a system that has a (pretty good btw) 96% chance to read an identifier correctly, you will get more and more false positives the more identifiers you scan.
That means expanding the Flock network also expands the amount of false positives.
This cannot be avoided, except if you are able to make the 96% rate better; but be reminded if this system would get upgraded from 96% to 99.6%, total precision would only increase about 1% (from 29.1% to 30.1%). reducing the number of false positives in this example by only 15 licence plates.
To actually reduce the amount of false positives, you would have to make the system less sensitive - which isn't possible in this context.